CRAN Package Check Results for Package immundata

Last updated on 2026-03-30 17:55:06 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.0.6	12.28	441.24	453.52	ERROR
r-devel-linux-x86_64-debian-gcc	0.0.6	8.31	386.63	394.94	ERROR
r-devel-linux-x86_64-fedora-clang	0.0.6	20.00	1179.84	1199.84	ERROR
r-devel-linux-x86_64-fedora-gcc	0.0.6	21.00	934.63	955.63	ERROR
r-devel-macos-arm64	0.0.6	3.00	118.00	121.00	ERROR
r-devel-windows-x86_64	0.0.6	13.00	358.00	371.00	OK
r-patched-linux-x86_64	0.0.6	11.88	534.29	546.17	ERROR
r-release-linux-x86_64	0.0.6	10.39	553.96	564.35	ERROR
r-release-macos-arm64	0.0.6	3.00	120.00	123.00	OK
r-release-macos-x86_64	0.0.6	9.00	537.00	546.00	OK
r-release-windows-x86_64	0.0.6	13.00	356.00	369.00	ERROR
r-oldrel-macos-arm64	0.0.6	3.00	130.00	133.00	NOTE
r-oldrel-macos-x86_64	0.0.6	9.00	556.00	565.00	NOTE
r-oldrel-windows-x86_64	0.0.6	18.00	478.00	496.00	ERROR

Check Details

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [347s/175s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc13223659/annotations.parquet] > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc13223659/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc13223659] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc13223659'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc13223659'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 9.1 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c33c53aaf9/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c33c53aaf9/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c33c53aaf9] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c33c53aaf9'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c33c53aaf9'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 11.3 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c3745e594f/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c3745e594f/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c3745e594f] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c3745e594f'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c3745e594f'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.91 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc72958c33/annotations.parquet] > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc72958c33/metadata.json] > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc72958c33] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc72958c33'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc72958c33'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 8.14 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc611c3fb6/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc611c3fb6/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc611c3fb6] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc611c3fb6'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc611c3fb6'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 7.64 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c349994219/annotations.parquet] > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c349994219/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c349994219] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c349994219'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c349994219'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 10.05 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc52b99460/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc52b99460/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc52b99460] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc52b99460'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc52b99460'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 7.61 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c36e1f7bf8/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c36e1f7bf8/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c36e1f7bf8] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c36e1f7bf8'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c36e1f7bf8'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.92 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc37b5ace5/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc37b5ace5/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc37b5ace5] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc37b5ace5'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc37b5ace5'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 7.77 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c335282801/annotations.parquet] > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc75bcb82e/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c335282801/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c335282801] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c335282801'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c335282801'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.74 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc75bcb82e/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc75bcb82e] > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc75bcb82e'] > test-agg-strata.R: 1. exclude_columns > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc75bcb82e'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 7.47 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: 2. filter_nonproductive > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc44cfdedc/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc44cfdedc/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc44cfdedc] > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc44cfdedc'] > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc44cfdedc'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 7.69 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c33bcad68a/annotations.parquet] > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c33bcad68a/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c33bcad68a] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c33bcad68a'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c33bcad68a'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.92 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc7444486/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc7444486/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc7444486] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc7444486'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc7444486'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 10.14 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c36498825f/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c36498825f/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c36498825f] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c36498825f'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c36498825f'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 10.13 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc1ffa97cb/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc1ffa97cb/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc1ffa97cb] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc1ffa97cb'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc1ffa97cb'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 10.28 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FAL > test-compute-collect-immundata.R: SE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c37ae0c310/annotations.parquet] > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c37ae0c310/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c37ae0c310] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c37ae0c310'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c37ae0c310'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 10.08 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc2d95a428/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc2d95a428/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc2d95a428] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc2d95a428'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc2d95a428'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 10.01 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c364d3f148/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c364d3f148/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c364d3f148] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c364d3f148'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c364d3f148'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 10.12 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Joining plan is ready > test-agg-strata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc1ffd5f7b/annotations.parquet] > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc1ffd5f7b/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc1ffd5f7b] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc1ffd5f7b'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc1ffd5f7b'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 10.09 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc4191772e/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c35a5c48a0/annotations.parquet] > test-filter-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc4191772e/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc4191772e] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc4191772e'] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc4191772e'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 7.79 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c35a5c48a0/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c35a5c48a0] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c35a5c48a0'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c35a5c48a0'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.92 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc141bcc43/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-exact.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc141bcc43/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc141bcc43] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc141bcc43'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc141bcc43'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 7.75 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c317d1fec/annotations.parquet] > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c317d1fec/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c317d1fec] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c317d1fec'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c317d1fec'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.94 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc73f9fe90/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc73f9fe90/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc73f9fe90] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc73f9fe90'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc73f9fe90'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 8.02 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c3fde7a48/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c3fde7a48/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c3fde7a48] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c3fde7a48'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c3fde7a48'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 10.17 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc666c17e6/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc666c17e6/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc666c17e6] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc666c17e6'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc666c17e6'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 7.78 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c37c5bf902/annotations.parquet] > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc515bef05/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c37c5bf902/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c37c5bf902] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c37c5bf902'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c37c5bf902'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 10.03 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc515bef05/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc515bef05] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc515bef05'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc515bef05'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 7.68 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc4f95e2fc/annotations.parquet] > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-regex.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc4f95e2fc/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc4f95e2fc] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc4f95e2fc'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc4f95e2fc'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 7.83 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c31826c9a7/annotations.parquet] > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c31826c9a7/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c31826c9a7] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c31826c9a7'] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c31826c9a7'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 9.91 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc3ee6f66b/annotations.parquet] > test-filter-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc3ee6f66b/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc3ee6f66b] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc3ee6f66b'] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/file3148bc3ee6f66b'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 7.76 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c3646f58dc/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c3646f58dc/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c3646f58dc] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c3646f58dc'] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/file3148c3646f58dc'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 7.81 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. /home/hornik/tmp/scratch/Rtmpee9fyV/file3148c375142769.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/test_immundata_3148c327760629/annotations.parquet] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/test_immundata_3148c327760629/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/test_immundata_3148c327760629] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/test_immundata_3148c327760629'] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/test_immundata_3148c327760629'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.5 secs > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpOfBBwl/legacy_v1_3148bc60aec5e9/annotations.parquet] Saving _problems/test-io-repertoires-agg-stepwise-125.R > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/Rtmpee9fyV/file3148c365c7b845.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpOfBBwl/legacy_v1_3148bc60aec5e9/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpOfBBwl/legacy_v1_3148bc60aec5e9] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/legacy_v1_3148bc60aec5e9'] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpee9fyV/test_immundata_3148c3168e4ac9/annotations.parquet] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/legacy_v1_3148bc60aec5e9'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.54 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpee9fyV/test_immundata_3148c3168e4ac9/metadata.json] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpOfBBwl/legacy_v1_3148bc60aec5e9'] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpee9fyV/test_immundata_3148c3168e4ac9] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/test_immundata_3148c3168e4ac9'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpee9fyV/test_immundata_3148c3168e4ac9'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.43 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: *** caught segfault *** > test-io-repertoires-agg.R: address 0x32, cause 'memory not mapped' > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible Error: ! testthat subprocess exited in file 'test-io-repertoires-agg.R'. Caused by error: ! R session crashed with exit code -11 Backtrace: ▆ 1. └─testthat::test_check("immundata") 2. └─testthat::test_dir(...) 3. └─testthat:::test_files(...) 4. └─testthat:::test_files_parallel(...) 5. ├─withr::with_dir(...) 6. │ └─base::force(code) 7. ├─testthat::with_reporter(...) 8. │ └─base::tryCatch(...) 9. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. └─testthat:::parallel_event_loop_chunky(queue, reporters, ".") 13. └─queue$poll(Inf) 14. └─base::lapply(...) 15. └─testthat (local) FUN(X[[i]], ...) 16. └─private$handle_error(msg, i) 17. └─cli::cli_abort(...) 18. └─rlang::abort(...) Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [318s/162s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec120433691173/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec120433691173/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec120433691173] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120433691173'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120433691173'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 3.46 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c1ae0c4d6/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c1ae0c4d6/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c1ae0c4d6] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c1ae0c4d6'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c1ae0c4d6'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.31 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c6b76a188/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c6b76a188/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c6b76a188] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c6b76a188'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c6b76a188'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.06 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec12046fa060f6/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec12046fa060f6/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec12046fa060f6] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec12046fa060f6'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec12046fa060f6'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.79 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c74131292/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c74131292/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c74131292] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c74131292'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c74131292'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.04 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec1204d2d9143/annotations.parquet] > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec1204d2d9143/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec1204d2d9143] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec1204d2d9143'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec1204d2d9143'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.17 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec12042455e5cf/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c3af413ad/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec12042455e5cf/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec12042455e5cf] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec12042455e5cf'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec12042455e5cf'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.13 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c3af413ad/metadata.json] > test-annotate-external.R: 1. exclude_columns > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c3af413ad] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c3af413ad'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c3af413ad'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.13 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec120457a137b2/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec120457a137b2/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec120457a137b2] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120457a137b2'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120457a137b2'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.32 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c2b1baa62/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c2b1baa62/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c2b1baa62] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c2b1baa62'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c2b1baa62'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.18 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec120429179d7d/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec120429179d7d/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec120429179d7d] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120429179d7d'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120429179d7d'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.19 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c538473ab/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c538473ab/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c538473ab] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c538473ab'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c538473ab'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.28 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec120476237d3a/annotations.parquet] > test-annotate-receptors.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec120476237d3a/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec120476237d3a] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120476237d3a'] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120476237d3a'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 3.34 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec12042d8c47c8/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec12042d8c47c8/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec12042d8c47c8] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec12042d8c47c8'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec12042d8c47c8'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 4.2 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c24aa6578/annotations.parquet] > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c24aa6578/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c24aa6578] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c24aa6578'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c24aa6578'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.13 secs > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec1204246288e1/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec1204246288e1/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec1204246288e1] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec1204246288e1'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec1204246288e1'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 4.61 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c1cea6198/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c1cea6198/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c1cea6198] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c1cea6198'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c1cea6198'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.17 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec120430bf069e/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec120430bf069e/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec120430bf069e] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120430bf069e'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120430bf069e'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 4.43 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c1a385082/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c1a385082/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c1a385082] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c1a385082'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c1a385082'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.04 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec1204694689a7/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec1204694689a7/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec1204694689a7] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec1204694689a7'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec1204694689a7'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 4.1 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c7b3b9b4f/annotations.parquet] > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c7b3b9b4f/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c7b3b9b4f] > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec120479af3587/annotations.parquet] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c7b3b9b4f'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c7b3b9b4f'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.05 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec120479af3587/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec120479af3587] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120479af3587'] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120479af3587'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 3.06 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec120437168458/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-exact.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec120437168458/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec120437168458] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120437168458'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120437168458'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 3.32 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c2fec0c39/annotations.parquet] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c2fec0c39/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c2fec0c39] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c2fec0c39'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c2fec0c39'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-agg-strata.R: i Time elapsed: 4.01 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec1204900692e/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec1204900692e/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec1204900692e] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec1204900692e'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec1204900692e'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 3.11 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c61f51432/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c61f51432/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c61f51432] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c61f51432'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c61f51432'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.37 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec1204349e0846/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec1204349e0846/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec1204349e0846] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec1204349e0846'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec1204349e0846'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 3.1 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c2987b556/annotations.parquet] > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec1204a08cb8d/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c2987b556/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c2987b556] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c2987b556'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c2987b556'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.35 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec1204a08cb8d/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec1204a08cb8d] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec1204a08cb8d'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec1204a08cb8d'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 3.45 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c272e09cf/annotations.parquet] > test-filter-immundata-regex.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c272e09cf/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c272e09cf] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c272e09cf'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c272e09cf'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 3.21 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec12044a37c33d/annotations.parquet] > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-immundata.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec12044a37c33d/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec12044a37c33d] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec12044a37c33d'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec12044a37c33d'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 4.12 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c2512f0e5/annotations.parquet] > test-filter-receptors.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c2512f0e5/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c2512f0e5] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c2512f0e5'] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c2512f0e5'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 2.97 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/filec120469e08230/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/tmp/RtmprT7zA4/filec120469e08230/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/RtmprT7zA4/filec120469e08230] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120469e08230'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/filec120469e08230'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 3.41 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. /tmp/RtmprT7zA4/filec120454f758c1.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c12043bae6e3c/annotations.parquet] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/legacy_v1_c122c789bf43d/annotations.parquet] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c12043bae6e3c/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c12043bae6e3c] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12043bae6e3c'] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12043bae6e3c'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.27 secs > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/legacy_v1_c122c789bf43d/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/legacy_v1_c122c789bf43d] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/legacy_v1_c122c789bf43d'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/legacy_v1_c122c789bf43d'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.56 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/legacy_v1_c122c789bf43d'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension Saving _problems/test-io-repertoires-agg-stepwise-125.R > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmprT7zA4/filec120414645a48.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c12046847330a/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c12046847330a/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c12046847330a] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12046847330a'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12046847330a'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.29 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmprT7zA4/filec120445096b3a.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.43 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c12042376daa5/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c12042376daa5/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c12042376daa5] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12042376daa5'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12042376daa5'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.03 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmprT7zA4/filec12047538e5d8.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.44 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c12043b3f4dc5/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c12043b3f4dc5/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c12043b3f4dc5] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12043b3f4dc5'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12043b3f4dc5'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.01 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmprT7zA4/filec12042543d566.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.42 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c12044bc346a4/annotations.parquet] > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c12044bc346a4/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c12044bc346a4] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12044bc346a4'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12044bc346a4'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.93 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmprT7zA4/filec12042d0b5c0f.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c120445aedc0e/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c120445aedc0e/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c120445aedc0e] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c120445aedc0e'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c120445aedc0e'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.01 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmprT7zA4/filec120446f417be.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-repertoires-agg.R: 1. exclude_columns > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c12045b709acd/annotations.parquet] > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c12045b709acd/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c12045b709acd] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12045b709acd'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12045b709acd'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.05 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.41 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-64.R Saving _problems/test-io-repertoires-agg-70.R Saving _problems/test-io-repertoires-agg-88.R Saving _problems/test-io-repertoires-agg-96.R > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmprT7zA4/filec120442ef66fd.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c120425f3920e/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c120425f3920e/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c120425f3920e] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c120425f3920e'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c120425f3920e'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.3 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmprT7zA4/filec1204bf35bd6.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c120478077697/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c120478077697/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c120478077697] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c120478077697'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c120478077697'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.27 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmprT7zA4/filec120454b6a52e.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.55 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c12047c94a752/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c12047c94a752/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c12047c94a752] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12047c94a752'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12047c94a752'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.95 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmprT7zA4/filec120429f928c8.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c1204294f9c39/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c1204294f9c39/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c1204294f9c39] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c1204294f9c39'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c1204294f9c39'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.04 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmprT7zA4/filec120451d5788b.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.47 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/treated/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/treated/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/treated/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectB'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c12046849a13b/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c12046849a13b/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c12046849a13b] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12046849a13b'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12046849a13b'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.92 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmprT7zA4/filec1204457a7974.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c12042ea76073/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.38 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c12042ea76073/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c12042ea76073] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12042ea76073'] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12042ea76073'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.05 secs > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmprT7zA4/filec12046267ac77.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c1204187f5560/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c1204187f5560/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c1204187f5560] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c1204187f5560'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c1204187f5560'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.19 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmprT7zA4/filec1204458d2fca.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c12042d64d866/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c12042d64d866/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c12042d64d866] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12042d64d866'] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12042d64d866'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: i Time elapsed: 0.94 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmprT7zA4/filec1204458d2fca.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.45 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c12046f51e951/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c12046f51e951/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c12046f51e951] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12046f51e951'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12046f51e951'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.04 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c12045f81afc4/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c12045f81afc4/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c12045f81afc4] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12045f81afc4'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12045f81afc4'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 1.47 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c11a0be8b/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c11a0be8b/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c11a0be8b] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c11a0be8b'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c11a0be8b'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.05 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c1204662f58c4/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.51 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectB/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectB/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectB/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c1204662f58c4/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c1204662f58c4] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c1204662f58c4'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c1204662f58c4'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: i Time elapsed: 2.76 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.46 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/ops/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/imd_snap_tests/projectA/snapshots/ops/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c1204649d8f90/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c1204649d8f90/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c1204649d8f90] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c1204649d8f90'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c1204649d8f90'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.77 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c2d538f0f/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c2d538f0f/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c2d538f0f] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c2d538f0f'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c2d538f0f'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.28 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c120452fbf07e/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c120452fbf07e/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c120452fbf07e] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c120452fbf07e'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c120452fbf07e'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.62 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/filec122c626a616a/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpwZw7M1/filec122c626a616a/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/filec122c626a616a] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c626a616a'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/filec122c626a616a'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.39 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c120425c64384/annotations.parquet] > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/test-exclude/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmpwZw7M1/test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.61 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c120425c64384/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c120425c64384] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c120425c64384'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c120425c64384'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.57 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmpwZw7M1/test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.84 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/test-exclude-rename/annotations.parquet] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c120412dae7b9/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmpwZw7M1/test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.61 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c120412dae7b9/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c120412dae7b9] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c120412dae7b9'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c120412dae7b9'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.55 secs > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c12041907934/annotations.parquet] > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/test_immundata_c122c69e75f62/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c12041907934/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c12041907934] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12041907934'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12041907934'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 22.72 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmpwZw7M1/test_immundata_c122c69e75f62/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/test_immundata_c122c69e75f62] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test_immundata_c122c69e75f62'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test_immundata_c122c69e75f62'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 22.91 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors Saving _problems/test-io-repertoires-processing-90.R Saving _problems/test-io-repertoires-processing-110.R > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/test_immundata_c122c3b50f600/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/RtmpwZw7M1/test_immundata_c122c3b50f600/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/test_immundata_c122c3b50f600] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test_immundata_c122c3b50f600'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test_immundata_c122c3b50f600'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 3.9 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /tmp/RtmpwZw7M1/filec122c24e7fb7.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/test_immundata_c122c658448f6/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/RtmpwZw7M1/test_immundata_c122c658448f6/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/test_immundata_c122c658448f6] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test_immundata_c122c658448f6'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test_immundata_c122c658448f6'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.27 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /tmp/RtmpwZw7M1/filec122c4500cfef.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/test_immundata_c122c7218614a/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/RtmpwZw7M1/test_immundata_c122c7218614a/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/test_immundata_c122c7218614a] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test_immundata_c122c7218614a'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test_immundata_c122c7218614a'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.3 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. > test-io-repertoires-schema-table.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [/tmp/RtmpwZw7M1/test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [/tmp/RtmpwZw7M1/test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [/tmp/RtmpwZw7M1/test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/RtmpwZw7M1/test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 1.8 secs > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c1204714fbdb5/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c1204714fbdb5/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c1204714fbdb5] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c1204714fbdb5'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c1204714fbdb5'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 21.99 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /tmp/RtmprT7zA4/filec120428be7ecb.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c12045da6738c/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c12045da6738c/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c12045da6738c] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12045da6738c'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c12045da6738c'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 0.93 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /tmp/RtmprT7zA4/filec12041508390b.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmprT7zA4/test_immundata_c1204755c28a/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmprT7zA4/test_immundata_c1204755c28a/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmprT7zA4/test_immundata_c1204755c28a] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c1204755c28a'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmprT7zA4/test_immundata_c1204755c28a'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 0.93 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 10 | WARN 0 | SKIP 0 | PASS 314 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-agg-stepwise.R:125:3'): agg_repertoires single-chain stepwise materialized path is stable ── <duckdb_error/rlang_error/error/condition> Error in `(function (context, message, error_type = NULL, raw_message = NULL, extra_info = NULL) { fields <- list() fields$context <- context fields$error_type <- error_type fields$raw_message <- raw_message fields$extra_info <- extra_info error_parts <- c(message, i = paste0("Context: ", context)) if (!is.null(error_type)) { error_parts <- c(error_parts, i = paste0("Error type: ", error_type)) } if (length(extra_info) > 0) { info_text <- paste0(names(extra_info), ": ", extra_info) names(info_text) <- rep_len("i", length(info_text)) error_parts <- c(error_parts, info_text) } rlang::abort(error_parts, class = "duckdb_error", !!!fields) })("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::ToJSON(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x54) [0x7fdee64a17b4]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::Exception(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7fdee64a17e1]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7fdee64a4851]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x1a9) [0x7fdee67b91d9]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(+0x90b74c) [0x7fdee590b74c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)+0x118) [0x7fdee70a48f8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::function<void (duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)> const&)+0x86) [0x7fdee70a6626]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x3f) [0x7fdee70a6bef]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x86) [0x7fdee67a6726]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7fdee70b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7fdee70b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7fdee70b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::allocator<unsigned long> >&)+0x3c) [0x7fdee70b348c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7fdee70b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7fdee70b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x8a) [0x7fdee67a711a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x2a) [0x7fdee67a730a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x691) [0x7fdee6e990b1]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x47a) [0x7fdee6e997fa]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0xae) [0x7fdee6e9ca7e]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xa3) [0x7fdee6e9cef3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0x8c) [0x7fdee6e9d11c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0x9b) [0x7fdee6e9ddeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x18b) [0x7fdee6ea0d3b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x7d) [0x7fdee6ea102d]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x51) [0x7fdee6ea1a21]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x137) [0x7fdee5bcfd97]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x2b1) [0x7fdee5bd04b1]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x45) [0x7fdee5bd0b95]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xa6add) [0x7fdf02aa6add]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7fdf02b5b739]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7fdf02ba6cc3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a7247) [0x7fdf02ba7247]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15f6a0) [0x7fdf02b5f6a0]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xa9a47) [0x7fdf02aa9a47]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7fdf02b5b739]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7fdf02ba6cc3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a73d9) [0x7fdf02ba73d9]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a763c) [0x7fdf02ba763c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c40f) [0x7fdf02b4c40f]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7fdf02b5b739]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7fdf02ba6cc3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a73d9) [0x7fdf02ba73d9]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a763c) [0x7fdf02ba763c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c40f) [0x7fdf02b4c40f]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15d16d) [0x7fdf02b5d16d]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7fdf02b582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7fdf02b5babc]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7fdf02b582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15e67f) [0x7fdf02b5e67f]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15eb44) [0x7fdf02b5eb44]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7fdf02b5babc]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7fdf02b582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xcff1e) [0x7fdf02acff1e]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xcff1e) [0x7fdf02acff1e]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1587f4) [0x7fdf02b587f4]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x158b05) [0x7fdf02b58b05]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x150a74) [0x7fdf02b50a74]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7fdf02b5babc]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7fdf02b582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1587f4) [0x7fdf02b587f4]\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors")`: Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference "imd_barcode" [42.0]: inequal types (VARCHAR != INTEGER) Stack Trace: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::ToJSON(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x54) [0x7fdee64a17b4] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::Exception(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7fdee64a17e1] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7fdee64a4851] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x1a9) [0x7fdee67b91d9] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(+0x90b74c) [0x7fdee590b74c] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)+0x118) [0x7fdee70a48f8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::function<void (duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)> const&)+0x86) [0x7fdee70a6626] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x3f) [0x7fdee70a6bef] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x86) [0x7fdee67a6726] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7fdee70b77bd] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7fdee70b77bd] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7fdee70b77bd] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::allocator<unsigned long> >&)+0x3c) [0x7fdee70b348c] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7fdee70b77bd] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7fdee70b77bd] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x8a) [0x7fdee67a711a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x2a) [0x7fdee67a730a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x691) [0x7fdee6e990b1] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x47a) [0x7fdee6e997fa] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0xae) [0x7fdee6e9ca7e] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xa3) [0x7fdee6e9cef3] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0x8c) [0x7fdee6e9d11c] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0x9b) [0x7fdee6e9ddeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x18b) [0x7fdee6ea0d3b] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x7d) [0x7fdee6ea102d] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x51) [0x7fdee6ea1a21] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x137) [0x7fdee5bcfd97] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x2b1) [0x7fdee5bd04b1] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x45) [0x7fdee5bd0b95] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xa6add) [0x7fdf02aa6add] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7fdf02b5b739] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7fdf02ba6cc3] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a7247) [0x7fdf02ba7247] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15f6a0) [0x7fdf02b5f6a0] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xa9a47) [0x7fdf02aa9a47] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7fdf02b5b739] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7fdf02ba6cc3] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a73d9) [0x7fdf02ba73d9] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a763c) [0x7fdf02ba763c] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c40f) [0x7fdf02b4c40f] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7fdf02b5b739] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7fdf02ba6cc3] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a73d9) [0x7fdf02ba73d9] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a763c) [0x7fdf02ba763c] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c40f) [0x7fdf02b4c40f] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15d16d) [0x7fdf02b5d16d] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7fdf02b582b7] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7fdf02b5babc] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7fdf02b582b7] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15e67f) [0x7fdf02b5e67f] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15eb44) [0x7fdf02b5eb44] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7fdf02b5babc] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7fdf02b582b7] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xcff1e) [0x7fdf02acff1e] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xcff1e) [0x7fdf02acff1e] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1587f4) [0x7fdf02b587f4] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x158b05) [0x7fdf02b58b05] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x150a74) [0x7fdf02b50a74] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7fdf02b5babc] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7fdf02b582b7] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1587f4) [0x7fdf02b587f4] This error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic. For more information, see https://duckdb.org/docs/stable/dev/internal_errors i Context: GetQueryResult Backtrace: ▆ 1. ├─dplyr::collect(single_chain_annotations) at test-io-repertoires-agg-stepwise.R:125:3 2. ├─duckplyr:::collect.prudent_duckplyr_df(single_chain_annotations) 3. │ ├─dplyr::collect(out) 4. │ └─duckplyr:::collect.duckplyr_df(out) 5. │ └─base::nrow(x) 6. │ ├─base::dim(x) 7. │ └─base::dim.data.frame(x) 8. │ └─base::.row_names_info(x, 2L) 9. └─duckdb (local) `<fn>`("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::ToJSON(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x54) [0x7fdee64a17b4]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::Exception(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7fdee64a17e1]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7fdee64a4851]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x1a9) [0x7fdee67b91d9]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(+0x90b74c) [0x7fdee590b74c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)+0x118) [0x7fdee70a48f8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::function<void (duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)> const&)+0x86) [0x7fdee70a6626]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x3f) [0x7fdee70a6bef]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x86) [0x7fdee67a6726]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7fdee70b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7fdee70b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7fdee70b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::allocator<unsigned long> >&)+0x3c) [0x7fdee70b348c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7fdee70b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7fdee70b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7fdee67a671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x8a) [0x7fdee67a711a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x2a) [0x7fdee67a730a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x691) [0x7fdee6e990b1]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x47a) [0x7fdee6e997fa]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0xae) [0x7fdee6e9ca7e]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xa3) [0x7fdee6e9cef3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0x8c) [0x7fdee6e9d11c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0x9b) [0x7fdee6e9ddeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x18b) [0x7fdee6ea0d3b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x7d) [0x7fdee6ea102d]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x51) [0x7fdee6ea1a21]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x137) [0x7fdee5bcfd97]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x2b1) [0x7fdee5bd04b1]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x45) [0x7fdee5bd0b95]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xa6add) [0x7fdf02aa6add]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7fdf02b5b739]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7fdf02ba6cc3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a7247) [0x7fdf02ba7247]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15f6a0) [0x7fdf02b5f6a0]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xa9a47) [0x7fdf02aa9a47]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7fdf02b5b739]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7fdf02ba6cc3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a73d9) [0x7fdf02ba73d9]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a763c) [0x7fdf02ba763c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c40f) [0x7fdf02b4c40f]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7fdf02b5b739]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7fdf02ba6cc3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a73d9) [0x7fdf02ba73d9]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a763c) [0x7fdf02ba763c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c40f) [0x7fdf02b4c40f]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15d16d) [0x7fdf02b5d16d]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7fdf02b582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7fdf02b5babc]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7fdf02b582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15e67f) [0x7fdf02b5e67f]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15eb44) [0x7fdf02b5eb44]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7fdf02b5babc]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7fdf02b582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xcff1e) [0x7fdf02acff1e]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xcff1e) [0x7fdf02acff1e]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7fdf02b4c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1587f4) [0x7fdf02b587f4]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x158b05) [0x7fdf02b58b05]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x150a74) [0x7fdf02b50a74]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7fdf02b57aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7fdf02b57ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7fdf02b59edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7fdf02b5acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7fdf02b5800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7fdf02b5babc]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7fdf02b582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1587f4) [0x7fdf02b587f4]\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors") 10. └─rlang::abort(error_parts, class = "duckdb_error", !!!fields) ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmprT7zA4/filec120414645a48.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmprT7zA4/filec120414645a48.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmprT7zA4/filec120414645a48.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmprT7zA4/filec120414645a48.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmprT7zA4/filec120414645a48.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmprT7zA4/filec120414645a48.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmprT7zA4/filec120414645a48.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmprT7zA4/filec120414645a48.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmprT7zA4/filec120414645a48.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmprT7zA4/filec120414645a48.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:205:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmprT7zA4/filec120414645a48.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmprT7zA4/filec120414645a48.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmprT7zA4/filec120414645a48.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmprT7zA4/filec120414645a48.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmprT7zA4/filec120414645a48.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmprT7zA4/filec120414645a48.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmprT7zA4/filec120414645a48.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmprT7zA4/filec120414645a48.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmprT7zA4/filec120414645a48.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmprT7zA4/filec120414645a48.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:208:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmprT7zA4/filec120414645a48.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmprT7zA4/filec120414645a48.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmprT7zA4/filec120414645a48.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmprT7zA4/filec120414645a48.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmprT7zA4/filec120414645a48.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmprT7zA4/filec120414645a48.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmprT7zA4/filec120414645a48.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmprT7zA4/filec120414645a48.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmprT7zA4/filec120414645a48.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmprT7zA4/filec120414645a48.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:212:5 ── Failure ('test-io-repertoires-agg.R:62:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample1 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:68:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample2_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample2 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:86:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count1[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 ── Failure ('test-io-repertoires-agg.R:94:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count2[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 ── Error ('test-io-repertoires-processing.R:87:3'): read_repertoires() removes non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:87:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires-processing.R:106:3'): read_repertoires() correctly reads non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:106:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) [ FAIL 10 | WARN 0 | SKIP 0 | PASS 314 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [17m/11m] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00eced38e3/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010684fbbba/annotations.parquet] > test-annotate-barcodes.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00eced38e3/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00eced38e3] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00eced38e3'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00eced38e3'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 17.48 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010684fbbba/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010684fbbba] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010684fbbba'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010684fbbba'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 18.32 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01040536acf/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01040536acf/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01040536acf] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01040536acf'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01040536acf'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 17.08 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e6eef6c93/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e6eef6c93/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e6eef6c93] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e6eef6c93'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e6eef6c93'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 15.61 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0107a7065bd/annotations.parquet] > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e6abe017b/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0107a7065bd/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0107a7065bd] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0107a7065bd'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0107a7065bd'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 20.57 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e6abe017b/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e6abe017b] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e6abe017b'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e6abe017b'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 15.67 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: SE` to quiet this message. > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e7c35ed58/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e7c35ed58/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e7c35ed58] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e7c35ed58'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e7c35ed58'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 15.93 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01077e0ebce/annotations.parquet] > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01077e0ebce/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01077e0ebce] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01077e0ebce'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01077e0ebce'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 18.11 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e58fb7bd2/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e58fb7bd2/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e58fb7bd2] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e58fb7bd2'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e58fb7bd2'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 15.5 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0107f507e25/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0107f507e25/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0107f507e25] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0107f507e25'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0107f507e25'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 18.52 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e2523413a/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e2523413a/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e2523413a] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e2523413a'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e2523413a'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 15.99 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0101de72ac2/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0101de72ac2/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0101de72ac2] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0101de72ac2'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0101de72ac2'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 19.31 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e555781e8/annotations.parquet] > test-annotate-receptors.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e555781e8/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e555781e8] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e555781e8'] > test-agg-strata.R: Rows: 2 Columns: 4 > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e555781e8'] > test-annotate-receptors.R: > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 17.13 secs > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010651ea5f3/annotations.parquet] > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e45a8f572/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010651ea5f3/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010651ea5f3] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010651ea5f3'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010651ea5f3'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 19.19 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e45a8f572/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e45a8f572] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e45a8f572'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e45a8f572'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 20.47 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e5d92dbdd/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e5d92dbdd/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e5d92dbdd] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e5d92dbdd'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e5d92dbdd'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 18.75 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-agg-strata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010272b1310/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010272b1310/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010272b1310] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010272b1310'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010272b1310'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 17.87 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e4ac257a/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e4ac257a/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e4ac257a] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e4ac257a'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e4ac257a'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 19.67 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Respons > test-compute-collect-immundata.R: e, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FAL > test-compute-collect-immundata.R: SE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0106e904ca7/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0106e904ca7/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0106e904ca7] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0106e904ca7'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0106e904ca7'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 18.44 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00ef8e7a74/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00ef8e7a74/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00ef8e7a74] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00ef8e7a74'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00ef8e7a74'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 19.66 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0106877115f/annotations.parquet] > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0106877115f/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0106877115f] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0106877115f'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0106877115f'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 18.25 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00eec3d53d/annotations.parquet] > test-filter-barcodes.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00eec3d53d/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00eec3d53d] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00eec3d53d'] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00eec3d53d'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 14.51 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0101daba2fd/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0101daba2fd/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0101daba2fd] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0101daba2fd'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0101daba2fd'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 17.46 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e620e23a7/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e620e23a7/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e620e23a7] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e620e23a7'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e620e23a7'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 14.6 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. > test-filter-immundata-hamm.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e43a97138/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0103fa7374f/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e43a97138/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e43a97138] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e43a97138'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e43a97138'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 13.49 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0103fa7374f/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0103fa7374f] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0103fa7374f'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0103fa7374f'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 20.86 secs > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e5d2dd808/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e5d2dd808/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e5d2dd808] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e5d2dd808'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e5d2dd808'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 14.97 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0101cb6ebe9/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0101cb6ebe9/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0101cb6ebe9] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0101cb6ebe9'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0101cb6ebe9'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 20.59 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e21f5fe55/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e21f5fe55/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e21f5fe55] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e21f5fe55'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e21f5fe55'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 17.96 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Respons > test-filter-immundata.R: e, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0104f9110a7/annotations.parquet] > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0104f9110a7/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0104f9110a7] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0104f9110a7'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0104f9110a7'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 13.76 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e272137a1/annotations.parquet] > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01051f60922/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e272137a1/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e272137a1] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e272137a1'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e272137a1'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 18.94 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-receptors.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01051f60922/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01051f60922] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01051f60922'] > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01051f60922'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 14.24 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/legacy_v1_1fc01044d9ae/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/legacy_v1_1fc01044d9ae/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/legacy_v1_1fc01044d9ae] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/legacy_v1_1fc01044d9ae'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/legacy_v1_1fc01044d9ae'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 6.62 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/legacy_v1_1fc01044d9ae'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 5.99 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e402428ec/annotations.parquet] > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e402428ec/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e402428ec] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e402428ec'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e402428ec'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 17.41 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e68ac82b6.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e1439addb/annotations.parq > test-io-repertoires-agg-stepwise.R: uet] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e1439addb/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e1439addb] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e1439addb'] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e1439addb'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 1.18 secs > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/annotations.parquet] Saving _problems/test-io-repertoires-agg-stepwise-125.R > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 6.24 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e1d1b5464/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e1d1b5464/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e1d1b5464] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e1d1b5464'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e1d1b5464'] > test-io-repertoires-agg.R: > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.34 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e485ad2cc.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 5.69 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e5208dc20/annotations.parq > test-io-repertoires-agg.R: uet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e5208dc20/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e5208dc20] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e5208dc20'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e5208dc20'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 5.18 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e2891a524.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e7f5573ae/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e7f5573ae/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e7f5573ae] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e7f5573ae'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e7f5573ae'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 4.86 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e18bb249d.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00ec7baba7/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00ec7baba7/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00ec7baba7] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00ec7baba7'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00ec7baba7'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/metadata.json] > test-io-repertoires-agg.R: i Time elapsed: 4.05 secs > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA] > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 14.75 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e130b5c40.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e127f50f3/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e127f50f3/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e127f50f3] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e127f50f3'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e127f50f3'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 4.2 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/metadata.json] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA] > test-io-repertoires-agg.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e3a78cf0f.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-repertoires-agg.R: v All files have the same extension > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-repertoires-agg.R: v Renaming is finished > test-io-immundata.R: i Time elapsed: 6.34 secs > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-repertoires-agg.R: 1. exclude_columns > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e618a41/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e618a41/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e618a41] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e618a41'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e618a41'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 3.56 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-64.R Saving _problems/test-io-repertoires-agg-70.R Saving _problems/test-io-repertoires-agg-88.R Saving _problems/test-io-repertoires-agg-96.R > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e6a00b9ca.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e12101fde/annotations.parq > test-io-repertoires-counts.R: uet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e12101fde/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e12101fde] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e12101fde'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e12101fde'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.88 secs > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e170519d7.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e70b604a9/annotations.parq > test-io-repertoires-counts.R: uet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e70b604a9/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e70b604a9] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e70b604a9'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e70b604a9'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.97 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-repertoires-counts.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e2d67fca7.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 6.62 secs > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/treated/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/treated/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/treated/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e2a18b1e0/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e2a18b1e0/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e2a18b1e0] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e2a18b1e0'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e2a18b1e0'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 3.49 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e55732b6a.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-immundata.R: i Time elapsed: 5.92 secs > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e3e4a3cdd/annotations.parquet] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e3e4a3cdd/metadata.json] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e3e4a3cdd] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e3e4a3cdd'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e3e4a3cdd'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 4.4 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e2985e57d.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e266bcc9c/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e266bcc9c/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e266bcc9c] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e266bcc9c'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e266bcc9c'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 3.91 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e61e4576f.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 7.07 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e139e4b6/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e139e4b6/metadata.json] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e139e4b6] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e139e4b6'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e139e4b6'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 3.66 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e3e4a9936.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e66864922/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e66864922/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e66864922] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e66864922'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e66864922'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.55 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e1e10f766.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e24e3d4ff/annotations.parq > test-io-repertoires-counts.R: uet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e24e3d4ff/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e24e3d4ff] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e24e3d4ff'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e24e3d4ff'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 3.24 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e1e10f766.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e4b72493f/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e4b72493f/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e4b72493f] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e4b72493f'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e4b72493f'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 4.11 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e496d27cb/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01044d445f3/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e496d27cb/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e496d27cb] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e496d27cb'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e496d27cb'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 6.05 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01044d445f3/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01044d445f3] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01044d445f3'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc01044d445f3'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 16.89 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 6.55 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectB/snapshots/baseline/v001'] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e4a770b75/annotations.parquet] > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e4a770b75/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e4a770b75] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e4a770b75'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e4a770b75'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 11.87 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 6.39 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/ops/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/imd_snap_tests/projectA/snapshots/ops/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e2c7dd5a2/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e2c7dd5a2/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e2c7dd5a2] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e2c7dd5a2'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e2c7dd5a2'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 11.21 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010ff5360e/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010ff5360e/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010ff5360e] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010ff5360e'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010ff5360e'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 15.84 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-files.R: v Joining plan is ready > test-io-immundata.R: v Preprocessing plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e2f8d967f/annotations.parquet] > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e2f8d967f/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e2f8d967f] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e2f8d967f'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e2f8d967f'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 14.6 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Respons > test-io-repertoires-files.R: e, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010312b589e/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010312b589e/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010312b589e] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010312b589e'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc010312b589e'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 14.28 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e48977e5/annotations.parqu > test-io-repertoires-files.R: et] > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-exclude/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e48977e5/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e48977e5] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e48977e5'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e48977e5'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 15.35 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 6.9 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 7.4 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e10044020/annotations.parq > test-io-repertoires-files.R: uet] > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-exclude-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 7.16 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e10044020/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e10044020] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e10044020'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e10044020'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-processing.R: > test-io-repertoires-files.R: i Time elapsed: 15.65 secs > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_ > test-io-repertoires-processing.R: 1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0 > test-io-repertoires-processing.R: _1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sam > test-io-repertoires-processing.R: ple_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 7.37 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/imm > test-io-repertoires-processing.R: undata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sam > test-io-repertoires-processing.R: ple_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sam > test-io-repertoires-processing.R: ple_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 5.95 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e12fd61e7/annotations.parquet] > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc010ce494d6/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e12fd61e7/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e12fd61e7] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e12fd61e7'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e12fd61e7'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.68 mins > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc010ce494d6/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc010ce494d6] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc010ce494d6'] > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc010ce494d6'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.5 mins > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc0106c294ae/annotations.parqu > test-io-repertoires-schema-single.R: et] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc0106c294ae/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc0106c294ae] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc0106c294ae'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc0106c294ae'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 14.97 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0105bf1931a.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc01036738a90/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc01036738a90/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc01036738a90] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc01036738a90'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc01036738a90'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 1.35 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/file1fc0104cd5b85c.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc0102956556/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc0102956556/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc0102956556] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc0102956556'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test_immundata_1fc0102956556'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 1.47 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. > test-io-repertoires-schema-table.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/Rtmpf2WWI0/test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 8.17 secs > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00ecc49763/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00ecc49763/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00ecc49763] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00ecc49763'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00ecc49763'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.52 mins > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e6966013a.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e3a8ca645/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e3a8ca645/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e3a8ca645] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e3a8ca645'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e3a8ca645'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 4.67 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e5540cb45.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e10afa720/annotations.parq > test-io-repertoires-schema-paired.R: uet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e10afa720/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e10afa720] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e10afa720'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/test_immundata_1fc00e10afa720'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 3.78 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-agg-stepwise.R:125:3'): agg_repertoires single-chain stepwise materialized path is stable ── <duckdb_error/rlang_error/error/condition> Error in `(function (context, message, error_type = NULL, raw_message = NULL, extra_info = NULL) { fields <- list() fields$context <- context fields$error_type <- error_type fields$raw_message <- raw_message fields$extra_info <- extra_info error_parts <- c(message, i = paste0("Context: ", context)) if (!is.null(error_type)) { error_parts <- c(error_parts, i = paste0("Error type: ", error_type)) } if (length(extra_info) > 0) { info_text <- paste0(names(extra_info), ": ", extra_info) names(info_text) <- rep_len("i", length(info_text)) error_parts <- c(error_parts, info_text) } rlang::abort(error_parts, class = "duckdb_error", !!!fields) })("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)+0x34) [0x7f7616275a44]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long&, unsigned long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long&, unsigned long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&&)+0xa6) [0x7f76166237c6]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitReplace(duckdb::BoundColumnRefExpression&, duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)+0x298) [0x7f7616605e78]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)+0x1c7) [0x7f7617169a77]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::__1::function<void (duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)> const&)+0x6fb) [0x7f761716973b]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x2a) [0x7f761716873a]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7c0) [0x7f7616605950]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f76171686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f76171686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f76171686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::__1::allocator<unsigned long> >&)+0x2e) [0x7f7617168c9e]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f76171686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f76171686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>)+0x75) [0x7f761661a4c5]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>)+0x2b) [0x7f761661a3db]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x655) [0x7f7616e9e775]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x40b) [0x7f7616e9f44b]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0x7b) [0x7f7616ea36cb]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0x113) [0x7f7616ea5813]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xaac) [0x7f7616ea30ec]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0x96) [0x7f7616ea4046]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x277) [0x7f7616ea8217]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x8c) [0x7f7616ea885c]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x80) [0x7f7616ecd7f0]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x1bd) [0x7f761574057d]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x303) [0x7f7615740073]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x44) [0x7f761573ec24]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x35277) [0x561961acd277]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x561961b61556]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x561961bc4642]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12bf65) [0x561961bc3f65]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe7c52) [0x561961b7fc52]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x39663) [0x561961ad1663]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x561961b61556]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x561961bc4642]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c069) [0x561961bc4069]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12cb9e) [0x561961bc4b9e]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfb06) [0x561961b67b06]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x561961b61556]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x561961bc4642]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c069) [0x561961bc4069]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12cb9e) [0x561961bc4b9e]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfb06) [0x561961b67b06]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5978) [0x561961b7d978]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561961b605e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x561961b7cabb]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561961b605e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe6de8) [0x561961b7ede8]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe71c8) [0x561961b7f1c8]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x561961b7cabb]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561961b605e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x55db0) [0x561961aeddb0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x55db0) [0x561961aeddb0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8e84) [0x561961b60e84]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcbe0) [0x561961b74be0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2b9) [0x561961b652b9]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x561961b7cabb]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561961b605e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8e84) [0x561961b60e84]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcbe0) [0x561961b74be0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2b9) [0x561961b652b9]\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors")`: Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference "imd_barcode" [42.0]: inequal types (VARCHAR != INTEGER) Stack Trace: /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)+0x34) [0x7f7616275a44] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long&, unsigned long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long&, unsigned long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&&)+0xa6) [0x7f76166237c6] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitReplace(duckdb::BoundColumnRefExpression&, duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)+0x298) [0x7f7616605e78] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)+0x1c7) [0x7f7617169a77] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::__1::function<void (duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)> const&)+0x6fb) [0x7f761716973b] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x2a) [0x7f761716873a] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7c0) [0x7f7616605950] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f76171686d4] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f76171686d4] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f76171686d4] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::__1::allocator<unsigned long> >&)+0x2e) [0x7f7617168c9e] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f76171686d4] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f76171686d4] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>)+0x75) [0x7f761661a4c5] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>)+0x2b) [0x7f761661a3db] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x655) [0x7f7616e9e775] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x40b) [0x7f7616e9f44b] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0x7b) [0x7f7616ea36cb] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0x113) [0x7f7616ea5813] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xaac) [0x7f7616ea30ec] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0x96) [0x7f7616ea4046] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x277) [0x7f7616ea8217] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x8c) [0x7f7616ea885c] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x80) [0x7f7616ecd7f0] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x1bd) [0x7f761574057d] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x303) [0x7f7615740073] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x44) [0x7f761573ec24] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x35277) [0x561961acd277] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x561961b61556] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x561961bc4642] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12bf65) [0x561961bc3f65] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe7c52) [0x561961b7fc52] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x39663) [0x561961ad1663] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x561961b61556] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x561961bc4642] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c069) [0x561961bc4069] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12cb9e) [0x561961bc4b9e] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfb06) [0x561961b67b06] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x561961b61556] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x561961bc4642] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c069) [0x561961bc4069] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12cb9e) [0x561961bc4b9e] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfb06) [0x561961b67b06] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5978) [0x561961b7d978] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561961b605e0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x561961b7cabb] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561961b605e0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe6de8) [0x561961b7ede8] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe71c8) [0x561961b7f1c8] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x561961b7cabb] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561961b605e0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x55db0) [0x561961aeddb0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x55db0) [0x561961aeddb0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8e84) [0x561961b60e84] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcbe0) [0x561961b74be0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2b9) [0x561961b652b9] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x561961b7cabb] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561961b605e0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8e84) [0x561961b60e84] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcbe0) [0x561961b74be0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2b9) [0x561961b652b9] This error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic. For more information, see https://duckdb.org/docs/stable/dev/internal_errors i Context: GetQueryResult Backtrace: ▆ 1. ├─dplyr::collect(single_chain_annotations) at test-io-repertoires-agg-stepwise.R:125:3 2. ├─duckplyr:::collect.prudent_duckplyr_df(single_chain_annotations) 3. │ ├─dplyr::collect(out) 4. │ └─duckplyr:::collect.duckplyr_df(out) 5. │ └─base::nrow(x) 6. │ ├─base::dim(x) 7. │ └─base::dim.data.frame(x) 8. │ └─base::.row_names_info(x, 2L) 9. └─duckdb (local) `<fn>`("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)+0x34) [0x7f7616275a44]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long&, unsigned long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long&, unsigned long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&&)+0xa6) [0x7f76166237c6]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitReplace(duckdb::BoundColumnRefExpression&, duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)+0x298) [0x7f7616605e78]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)+0x1c7) [0x7f7617169a77]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::__1::function<void (duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)> const&)+0x6fb) [0x7f761716973b]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x2a) [0x7f761716873a]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7c0) [0x7f7616605950]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f76171686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f76171686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f76171686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::__1::allocator<unsigned long> >&)+0x2e) [0x7f7617168c9e]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f76171686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f76171686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f7616605945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>)+0x75) [0x7f761661a4c5]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>)+0x2b) [0x7f761661a3db]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x655) [0x7f7616e9e775]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x40b) [0x7f7616e9f44b]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0x7b) [0x7f7616ea36cb]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0x113) [0x7f7616ea5813]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xaac) [0x7f7616ea30ec]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0x96) [0x7f7616ea4046]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x277) [0x7f7616ea8217]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x8c) [0x7f7616ea885c]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x80) [0x7f7616ecd7f0]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x1bd) [0x7f761574057d]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x303) [0x7f7615740073]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x44) [0x7f761573ec24]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x35277) [0x561961acd277]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x561961b61556]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x561961bc4642]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12bf65) [0x561961bc3f65]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe7c52) [0x561961b7fc52]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x39663) [0x561961ad1663]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x561961b61556]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x561961bc4642]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c069) [0x561961bc4069]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12cb9e) [0x561961bc4b9e]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfb06) [0x561961b67b06]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x561961b61556]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x561961bc4642]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c069) [0x561961bc4069]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12cb9e) [0x561961bc4b9e]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfb06) [0x561961b67b06]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5978) [0x561961b7d978]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561961b605e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x561961b7cabb]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561961b605e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe6de8) [0x561961b7ede8]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe71c8) [0x561961b7f1c8]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x561961b7cabb]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561961b605e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x55db0) [0x561961aeddb0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x55db0) [0x561961aeddb0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x561961b678a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8e84) [0x561961b60e84]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcbe0) [0x561961b74be0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2b9) [0x561961b652b9]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x561961b60c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561961b603b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x561961b78449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x561961b7794c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561961b60806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x561961b7cabb]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561961b605e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8e84) [0x561961b60e84]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcbe0) [0x561961b74be0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2b9) [0x561961b652b9]\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors") 10. └─rlang::abort(error_parts, class = "duckdb_error", !!!fields) ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:205:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:208:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmpAiq38k/working_dir/RtmpzQAVyQ/file1fc00e29704c6c.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:212:5 ── Failure ('test-io-repertoires-agg.R:62:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample1 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:68:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample2_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample2 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:86:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count1[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 ── Failure ('test-io-repertoires-agg.R:94:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count2[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [13m/15m] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 7. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926d9acbd3/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926d9acbd3/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926d9acbd3] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926d9acbd3'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926d9acbd3'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 17.69 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79051bd943e/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79051bd943e/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79051bd943e] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79051bd943e'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79051bd943e'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 25.87 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792363e61d3/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792363e61d3/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792363e61d3] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792363e61d3'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792363e61d3'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 14.51 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907dfbbe0f/annotations.parquet] > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907dfbbe0f/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907dfbbe0f] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907dfbbe0f'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907dfbbe0f'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 30.03 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792463f8a28/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792463f8a28/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792463f8a28] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792463f8a28'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792463f8a28'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 16.77 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79237f55209/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79237f55209/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79237f55209] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79237f55209'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79237f55209'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 13.55 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902cb48d71/annotations.parquet] > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902cb48d71/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902cb48d71] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902cb48d71'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902cb48d71'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 25.19 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235eefab5/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235eefab5/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235eefab5] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235eefab5'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235eefab5'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 14.11 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79268757dd4/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7904aac5f0e/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79268757dd4/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79268757dd4] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79268757dd4'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79268757dd4'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 16.01 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7904aac5f0e/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7904aac5f0e] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7904aac5f0e'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7904aac5f0e'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 23.54 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-agg-strata.R: Rows: 2 Columns: 4 > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79277fdda51/annotations.parquet] > test-annotate-receptors.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79277fdda51/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79277fdda51] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79277fdda51'] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79277fdda51'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 14.54 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FAL > test-compute-collect-immundata.R: SE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907234acfe/annotations.parquet] > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79212852720/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907234acfe/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907234acfe] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907234acfe'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907234acfe'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 28.34 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79212852720/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79212852720] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79212852720'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79212852720'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 16.97 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924c4f5663/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924c4f5663/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924c4f5663] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924c4f5663'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924c4f5663'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 16.35 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907ca88ea1/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907ca88ea1/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907ca88ea1] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907ca88ea1'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907ca88ea1'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 25.07 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927d096fc3/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927d096fc3/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927d096fc3] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927d096fc3'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927d096fc3'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 18.33 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FAL > test-compute-collect-immundata.R: SE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926640ef44/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926640ef44/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926640ef44] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926640ef44'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926640ef44'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 19.32 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902899a603/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902899a603/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902899a603] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902899a603'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902899a603'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 21.03 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922974e07b/annotations.parquet] > test-filter-barcodes.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922974e07b/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922974e07b] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922974e07b'] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922974e07b'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 12.71 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924d9d00f4/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-exact.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924d9d00f4/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924d9d00f4] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924d9d00f4'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924d9d00f4'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 21.45 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. > test-filter-immundata-hamm.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790689f60fb/annotations.parquet] > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790689f60fb/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790689f60fb] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790689f60fb'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790689f60fb'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 22.02 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79256fdde69/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79256fdde69/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79256fdde69] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79256fdde69'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79256fdde69'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 17.86 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7903a74680a/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7903a74680a/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7903a74680a] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7903a74680a'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7903a74680a'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 25.86 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922898512e/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922898512e/metadata.json] > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922898512e] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922898512e'] > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922898512e'] > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: i Time elapsed: 14.68 secs > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79236c2bafd/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79236c2bafd/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79236c2bafd] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79236c2bafd'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79236c2bafd'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 15.84 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790532f86c5/annotations.parquet] > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926e086477/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790532f86c5/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790532f86c5] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790532f86c5'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790532f86c5'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 28.53 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926e086477/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926e086477] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926e086477'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926e086477'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 10.26 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FAL > test-filter-immundata.R: SE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-filter-immundata.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-immundata.R: 2. filter_nonproductive > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927e329b63/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927e329b63/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927e329b63] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927e329b63'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927e329b63'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 17.89 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79242a04fa1/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79046718a3c/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79242a04fa1/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79242a04fa1] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79242a04fa1'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79242a04fa1'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 12.96 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79046718a3c/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79046718a3c] > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79046718a3c'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79046718a3c'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 32.83 secs > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: 2. filter_nonproductive > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235be0531/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235be0531/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235be0531] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235be0531'] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235be0531'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 15.73 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/legacy_v1_27d7927bee8f5c/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/legacy_v1_27d7927bee8f5c/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/legacy_v1_27d7927bee8f5c] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/legacy_v1_27d7927bee8f5c'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/legacy_v1_27d7927bee8f5c'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 5.35 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/legacy_v1_27d7927bee8f5c'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.4 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-agg-strata.R: 1. prefix_barcodes > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 7.93 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790a667ad3/annotations.parquet] > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790a667ad3/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790a667ad3] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790a667ad3'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790a667ad3'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 33.42 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 8.67 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-agg-strata.R: 2. filter_nonproductive > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79048da6beb/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 18.89 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79048da6beb/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79048da6beb] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79048da6beb'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79048da6beb'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 22.09 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79016200e56.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7903532b234/annotations.parquet] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7903532b234/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7903532b234] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7903532b234'] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7903532b234'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 1.94 secs > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors Saving _problems/test-io-repertoires-agg-stepwise-125.R > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv > test-io-immundata.R: i Time elapsed: 9.56 secs > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v00 > test-io-immundata.R: 1/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v00 > test-io-immundata.R: 2/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790664c0555/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790664c0555/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790664c0555] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790664c0555'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790664c0555'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.05 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907846cb0e.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 9.19 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905b6c363e/annotations.parquet] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/treated/v001 > test-io-immundata.R: /annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905b6c363e/metadata.json] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905b6c363e] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/treated/v001] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905b6c363e'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/treated/v001'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905b6c363e'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 5.76 secs > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/annotations.parquet] > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79019eaec78.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 6.74 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v00 > test-io-immundata.R: 1/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v00 > test-io-immundata.R: 2/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790570e6e64/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790570e6e64/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790570e6e64] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790570e6e64'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790570e6e64'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 9.28 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7904b5e1971.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 6.86 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v00 > test-io-immundata.R: 1/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901913eefa/annotations.parquet] > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901913eefa/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901913eefa] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901913eefa'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901913eefa'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 7.15 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7906f49ea23.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ca52421/annotations.parq > test-io-repertoires-agg.R: uet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7925bafd3c6/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ca52421/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ca52421] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ca52421'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ca52421'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 9.48 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79074551a6e.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-repertoires-agg.R: 1. exclude_columns > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7925bafd3c6/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7925bafd3c6] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7925bafd3c6'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7925bafd3c6'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 18.8 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904e1b9dc7/annotations.parquet] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 7.92 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v00 > test-io-immundata.R: 1/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/snapshots/baseline/v00 > test-io-immundata.R: 1/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904e1b9dc7/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904e1b9dc7] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904e1b9dc7'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904e1b9dc7'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 13.06 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-64.R Saving _problems/test-io-repertoires-agg-70.R Saving _problems/test-io-repertoires-agg-88.R Saving _problems/test-io-repertoires-agg-96.R > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907da37725.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 5.46 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790444b60b6/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/ops/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/ops/v001'] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790444b60b6/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790444b60b6] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790444b60b6'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790444b60b6'] > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.71 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7903294b521.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ec722f/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ec722f/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ec722f] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ec722f'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ec722f'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.19 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79066e64c6f.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924fa94d3/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901cf40a2f/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901cf40a2f/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901cf40a2f] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901cf40a2f'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901cf40a2f'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 11.13 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924fa94d3/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924fa94d3] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924fa94d3'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924fa94d3'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 14.85 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7901a50e3a8.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-immundata.R: v Renaming is finished > test-io-repertoires-counts.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904cf22ab1/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904cf22ab1/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904cf22ab1] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904cf22ab1'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904cf22ab1'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 8.49 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7906482be5.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792785862c4/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792785862c4/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792785862c4] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792785862c4'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792785862c4'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 14.34 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7921f1c9deb/annotations.parquet] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906c53502f/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7921f1c9deb/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7921f1c9deb] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7921f1c9deb'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7921f1c9deb'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 8.77 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906c53502f/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906c53502f] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906c53502f'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906c53502f'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 14.45 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7903e35e67e.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924b6992cc/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790207c37cf/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924b6992cc/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924b6992cc] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924b6992cc'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924b6992cc'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 13.75 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790207c37cf/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790207c37cf] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790207c37cf'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790207c37cf'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 12.42 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79052b879fe.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790349b89c0/annotations.parq > test-io-repertoires-counts.R: uet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790349b89c0/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790349b89c0] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790349b89c0'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790349b89c0'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.96 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79020b2eca8.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79266e07a20/annotations.parq > test-io-repertoires-files.R: uet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79076bfb7b4/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79076bfb7b4/metadata.json] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79266e07a20/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79076bfb7b4] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79076bfb7b4'] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79266e07a20] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79266e07a20'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79076bfb7b4'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79266e07a20'] > test-io-repertoires-counts.R: i Time elapsed: 9.08 secs > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-files.R: i Time elapsed: 12.62 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79020b2eca8.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790c2c08bc/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790c2c08bc/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790c2c08bc] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790c2c08bc'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790c2c08bc'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: i Time elapsed: 10.97 secs > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792df7b924/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792df7b924/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792df7b924] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792df7b924'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792df7b924'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 17.24 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 10.41 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79255118757/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79255118757/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79255118757] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79255118757'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79255118757'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 15.82 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 14.13 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 10.61 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7927635141f/annotations.parquet] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7927635141f/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7927635141f] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7927635141f'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7927635141f'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 17.29 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_ > test-io-repertoires-processing.R: 1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 17.81 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FAL > test-io-repertoires-processing.R: SE` to quiet this message. > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/imm > test-io-repertoires-processing.R: undata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sam > test-io-repertoires-processing.R: ple_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 14.9 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoi > test-io-repertoires-processing.R: re_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FAL > test-io-repertoires-processing.R: SE` to quiet this message. > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FAL > test-io-repertoires-processing.R: SE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792782cba21/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792782cba21/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792782cba21] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792782cba21'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792782cba21'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.74 mins > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79071eb7c22/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79071eb7c22/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79071eb7c22] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79071eb7c22'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79071eb7c22'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.61 mins > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79074e4b8b9/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79074e4b8b9/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79074e4b8b9] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79074e4b8b9'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79074e4b8b9'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 21.93 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7906e9369c6.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905df630a5/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905df630a5/metadata.json] > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905df630a5] > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79262e5e50b/annotations.parq > test-io-repertoires-schema-paired.R: uet] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905df630a5'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905df630a5'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 1.34 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790707ccc2.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906b2315fe/annotations.parq > test-io-repertoires-schema-single.R: uet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906b2315fe/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906b2315fe] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906b2315fe'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906b2315fe'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 1.96 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. > test-io-repertoires-schema-table.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79262e5e50b/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79262e5e50b] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79262e5e50b'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79262e5e50b'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 2.24 mins > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-table.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-no-barcodes'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-paired.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7925bab20eb.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-table.R: i Time elapsed: 14.7 secs > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79215fff633/annotations.parquet] > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79215fff633/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79215fff633] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79215fff633'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79215fff633'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 9.66 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924674c7b4.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924ace5889/annotations.parquet] > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924ace5889/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924ace5889] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924ace5889'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924ace5889'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 7.21 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-agg-stepwise.R:125:3'): agg_repertoires single-chain stepwise materialized path is stable ── <duckdb_error/rlang_error/error/condition> Error in `(function (context, message, error_type = NULL, raw_message = NULL, extra_info = NULL) { fields <- list() fields$context <- context fields$error_type <- error_type fields$raw_message <- raw_message fields$extra_info <- extra_info error_parts <- c(message, i = paste0("Context: ", context)) if (!is.null(error_type)) { error_parts <- c(error_parts, i = paste0("Error type: ", error_type)) } if (length(extra_info) > 0) { info_text <- paste0(names(extra_info), ": ", extra_info) names(info_text) <- rep_len("i", length(info_text)) error_parts <- c(error_parts, info_text) } rlang::abort(error_parts, class = "duckdb_error", !!!fields) })("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Exception::ToJSON(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x66) [0x7f8cffc20186]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Exception::Exception(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x23) [0x7f8cffc201e3]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x15) [0x7f8cffc236c5]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x1ba) [0x7f8cfff7631a]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(+0x34914f) [0x7f8cfef4914f]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)+0x136) [0x7f8d008ef736]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::function<void (duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)> const&)+0x95) [0x7f8d008f18a5]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x51) [0x7f8d008f1e71]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x96) [0x7f8cfff628d6]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::allocator<unsigned long> >&)+0x4c) [0x7f8d008ff43c]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x9d) [0x7f8cfff632fd]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x39) [0x7f8cfff634f9]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x695) [0x7f8d006bb065]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x4ea) [0x7f8d006bb87a]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0xaf) [0x7f8d006befcf]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xbf) [0x7f8d006bf43f]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xa8) [0x7f8d006bf6c8]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0xb4) [0x7f8d006c0464]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x1bd) [0x7f8d006c399d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x92) [0x7f8d006c3d02]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x62) [0x7f8d006c4782]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x148) [0x7f8cff2dfe68]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x2df) [0x7f8cff2e05ff]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x6f) [0x7f8cff2e0f6f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x43b61a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544d22]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e283d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x43e43a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544e63]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x545122]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edbdc]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544e63]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x545122]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edbdc]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4df445]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e1c0f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e1f18]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x46976f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x46976f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d9e15]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e60bc]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4f12d1]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d9e15]\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors")`: Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference "imd_barcode" [42.0]: inequal types (VARCHAR != INTEGER) Stack Trace: /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Exception::ToJSON(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x66) [0x7f8cffc20186] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Exception::Exception(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x23) [0x7f8cffc201e3] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x15) [0x7f8cffc236c5] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x1ba) [0x7f8cfff7631a] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(+0x34914f) [0x7f8cfef4914f] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)+0x136) [0x7f8d008ef736] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::function<void (duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)> const&)+0x95) [0x7f8d008f18a5] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x51) [0x7f8d008f1e71] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x96) [0x7f8cfff628d6] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::allocator<unsigned long> >&)+0x4c) [0x7f8d008ff43c] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x9d) [0x7f8cfff632fd] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x39) [0x7f8cfff634f9] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x695) [0x7f8d006bb065] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x4ea) [0x7f8d006bb87a] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0xaf) [0x7f8d006befcf] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xbf) [0x7f8d006bf43f] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xa8) [0x7f8d006bf6c8] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0xb4) [0x7f8d006c0464] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x1bd) [0x7f8d006c399d] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x92) [0x7f8d006c3d02] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x62) [0x7f8d006c4782] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x148) [0x7f8cff2dfe68] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x2df) [0x7f8cff2e05ff] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x6f) [0x7f8cff2e0f6f] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x43b61a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x544d22] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e283d] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x43e43a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x544e63] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x545122] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edbdc] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x544e63] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x545122] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edbdc] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4df445] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e1c0f] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e1f18] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x46976f] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x46976f] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d9e15] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e60bc] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4f12d1] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d9e15] This error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic. For more information, see https://duckdb.org/docs/stable/dev/internal_errors i Context: GetQueryResult Backtrace: ▆ 1. ├─dplyr::collect(single_chain_annotations) at test-io-repertoires-agg-stepwise.R:125:3 2. ├─duckplyr:::collect.prudent_duckplyr_df(single_chain_annotations) 3. │ ├─dplyr::collect(out) 4. │ └─duckplyr:::collect.duckplyr_df(out) 5. │ └─base::nrow(x) 6. │ ├─base::dim(x) 7. │ └─base::dim.data.frame(x) 8. │ └─base::.row_names_info(x, 2L) 9. └─duckdb (local) `<fn>`("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Exception::ToJSON(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x66) [0x7f8cffc20186]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Exception::Exception(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x23) [0x7f8cffc201e3]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x15) [0x7f8cffc236c5]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x1ba) [0x7f8cfff7631a]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(+0x34914f) [0x7f8cfef4914f]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)+0x136) [0x7f8d008ef736]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::function<void (duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)> const&)+0x95) [0x7f8d008f18a5]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x51) [0x7f8d008f1e71]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x96) [0x7f8cfff628d6]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::allocator<unsigned long> >&)+0x4c) [0x7f8d008ff43c]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x9d) [0x7f8cfff632fd]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x39) [0x7f8cfff634f9]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x695) [0x7f8d006bb065]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x4ea) [0x7f8d006bb87a]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0xaf) [0x7f8d006befcf]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xbf) [0x7f8d006bf43f]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xa8) [0x7f8d006bf6c8]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0xb4) [0x7f8d006c0464]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x1bd) [0x7f8d006c399d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x92) [0x7f8d006c3d02]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x62) [0x7f8d006c4782]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x148) [0x7f8cff2dfe68]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x2df) [0x7f8cff2e05ff]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x6f) [0x7f8cff2e0f6f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x43b61a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544d22]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e283d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x43e43a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544e63]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x545122]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edbdc]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544e63]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x545122]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edbdc]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4df445]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e1c0f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e1f18]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x46976f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x46976f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d9e15]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e60bc]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4f12d1]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d9e15]\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors") 10. └─rlang::abort(error_parts, class = "duckdb_error", !!!fields) ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:205:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:208:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:212:5 ── Failure ('test-io-repertoires-agg.R:62:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample1 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:68:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample2_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample2 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:86:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count1[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 ── Failure ('test-io-repertoires-agg.R:94:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count2[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [187s/93s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f7e8b059d/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f7e8b059d/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f7e8b059d] > test-annotate-barcodes.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f7e8b059d'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f7e8b059d'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 2.24 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file23111f91e57f/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file23111f91e57f/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file23111f91e57f] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23111f91e57f'] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23111f91e57f'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 2.85 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file23113cdebaf4/annotations.parquet] > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f7b243a74/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file23113cdebaf4/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file23113cdebaf4] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23113cdebaf4'] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23113cdebaf4'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 2.84 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f7b243a74/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f7b243a74] > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f7b243a74'] > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f7b243a74'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 2.33 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f610cb573/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f610cb573/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f610cb573] > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f610cb573'] > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f610cb573'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 2.17 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file231159e153c1/annotations.parquet] > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file231159e153c1/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file231159e153c1] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231159e153c1'] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231159e153c1'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 2.82 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f312eb256/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f312eb256/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f312eb256] > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f312eb256'] > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f312eb256'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 2.16 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file231120ea53a5/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file231120ea53a5/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file231120ea53a5] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231120ea53a5'] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231120ea53a5'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 2.83 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f6fdbf2cc/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f6fdbf2cc/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f6fdbf2cc] > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f6fdbf2cc'] > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f6fdbf2cc'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 2.17 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file23114a525486/annotations.parquet] > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f73c44b61/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file23114a525486/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file23114a525486] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23114a525486'] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23114a525486'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 2.84 secs > test-annotate-external.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f73c44b61/metadata.json] > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f73c44b61] > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f73c44b61'] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f73c44b61'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 2.16 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-agg-strata.R: 2. filter_nonproductive > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f53c6a23c/annotations.parquet] > test-annotate-receptors.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f53c6a23c/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f53c6a23c] > test-annotate-receptors.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f53c6a23c'] > test-annotate-receptors.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f53c6a23c'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 2.16 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file23115795105/annotations.parquet] > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file23115795105/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file23115795105] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23115795105'] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23115795105'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 2.82 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f5572599f/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f5572599f/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f5572599f] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f5572599f'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f5572599f'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 2.83 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file23114b4dcd97/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file23114b4dcd97/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file23114b4dcd97] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23114b4dcd97'] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23114b4dcd97'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 2.82 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f1159d077/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f1159d077/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f1159d077] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f1159d077'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f1159d077'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 2.83 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file23117a376702/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file23117a376702/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file23117a376702] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23117a376702'] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23117a376702'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 2.83 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f6e85b71e/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f6e85b71e/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f6e85b71e] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f6e85b71e'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f6e85b71e'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 2.83 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file231160d3385c/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file231160d3385c/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file231160d3385c] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231160d3385c'] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231160d3385c'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 2.83 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f392e3675/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f392e3675/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f392e3675] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f392e3675'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f392e3675'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 2.84 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file231115be3455/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file231115be3455/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file231115be3455] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231115be3455'] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231115be3455'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 2.84 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f322c7ee3/annotations.parquet] > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-barcodes.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f322c7ee3/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f322c7ee3] > test-filter-barcodes.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f322c7ee3'] > test-filter-barcodes.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f322c7ee3'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 2.16 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f227f1aa9/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-exact.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f227f1aa9/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f227f1aa9] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f227f1aa9'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f227f1aa9'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 2.17 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file231125d9d3f3/annotations.parquet] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. > test-filter-immundata-hamm.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file231125d9d3f3/metadata.json] > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file231125d9d3f3] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231125d9d3f3'] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231125d9d3f3'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 2.84 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f3cbab83c/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f3cbab83c/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f3cbab83c] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f3cbab83c'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f3cbab83c'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 2.16 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311514b5982/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311514b5982/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311514b5982] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311514b5982'] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311514b5982'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 2.83 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f54b336a4/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f54b336a4/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f54b336a4] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f54b336a4'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f54b336a4'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 2.19 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311343b8751/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311343b8751/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311343b8751] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311343b8751'] > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311343b8751'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 2.84 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f4cb52675/annotations.parquet] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata-lev.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f4cb52675/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f4cb52675] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f4cb52675'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f4cb52675'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 2.16 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file231164ca8469/annotations.parquet] > test-filter-immundata-regex.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file231164ca8469/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file231164ca8469] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231164ca8469'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231164ca8469'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 2.2 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f58a2fdaf/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f58a2fdaf/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f58a2fdaf] > test-filter-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f58a2fdaf'] > test-filter-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f58a2fdaf'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 2.81 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311378a47ff/annotations.parquet] > test-filter-receptors.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311378a47ff/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311378a47ff] > test-filter-receptors.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311378a47ff'] > test-filter-receptors.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311378a47ff'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 2.2 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f44d39ad4/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/legacy_v1_231113301623/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f44d39ad4/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f44d39ad4] > test-filter-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f44d39ad4'] > test-filter-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f44d39ad4'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 2.18 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f7e35cd23.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3acb60a4/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/legacy_v1_231113301623/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/legacy_v1_231113301623] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/legacy_v1_231113301623'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/legacy_v1_231113301623'] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3acb60a4/metadata.json] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3acb60a4] > test-io-immundata.R: i Time elapsed: 0.97 secs > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3acb60a4'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3acb60a4'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.09 secs > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/legacy_v1_231113301623'] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible Saving _problems/test-io-repertoires-agg-stepwise-125.R > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f2ecd8018/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f2ecd8018/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f2ecd8018] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f2ecd8018'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f2ecd8018'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.08 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f55edf0bd.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f59fe8963/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f59fe8963/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f59fe8963] > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f59fe8963'] > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f59fe8963'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.32 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA] > test-io-repertoires-agg.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f63140bec.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 0.98 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f51d898be/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f51d898be/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f51d898be] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f51d898be'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f51d898be'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.3 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f3840c472.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f76fba8e/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f76fba8e/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f76fba8e] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f76fba8e'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f76fba8e'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.26 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f78438bc2.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 0.98 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f381ef476/annotations.parquet] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f381ef476/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f381ef476] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f381ef476'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f381ef476'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.33 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f3d5de9c4.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-repertoires-agg.R: 1. exclude_columns > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3898e2fb/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3898e2fb/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3898e2fb] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3898e2fb'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3898e2fb'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.32 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-64.R Saving _problems/test-io-repertoires-agg-70.R Saving _problems/test-io-repertoires-agg-88.R Saving _problems/test-io-repertoires-agg-96.R > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230ff2f326c.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f572255cd/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f572255cd/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f572255cd] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f572255cd'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f572255cd'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.08 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f66b020bc.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1110cfa4/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1110cfa4/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1110cfa4] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1110cfa4'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1110cfa4'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.09 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f49c92ba5.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 0.99 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f67449da2/annotations.parquet] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f67449da2/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f67449da2] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f67449da2'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f67449da2'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.3 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f43dc476f.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f4c680fa9/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f4c680fa9/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f4c680fa9] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f4c680fa9'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f4c680fa9'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.27 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f75e8f74f.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f7a3a0049/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f7a3a0049/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f7a3a0049] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f7a3a0049'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f7a3a0049'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.28 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f25d33203.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f622bbe2f/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f622bbe2f/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f622bbe2f] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f622bbe2f'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f622bbe2f'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.33 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f3f94e743.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f40ff664b/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f40ff664b/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f40ff664b] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f40ff664b'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f40ff664b'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.05 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f33ddb98e.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f74dd51b3/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f74dd51b3/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f74dd51b3] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f74dd51b3'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f74dd51b3'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.27 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f33ddb98e.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6e1efab5/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6e1efab5/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6e1efab5] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6e1efab5'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6e1efab5'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.33 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.41 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f78bb9ffc/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f78bb9ffc/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f78bb9ffc] > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f78bb9ffc'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f78bb9ffc'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 0.97 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 0.97 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-files.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f16c5ec7a/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 0.98 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/treated/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/treated/v001] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/treated/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-files.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f16c5ec7a/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f16c5ec7a] > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f16c5ec7a'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f16c5ec7a'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 1.87 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 0.99 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f440949ff/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f440949ff/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f440949ff] > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f440949ff'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f440949ff'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 1.87 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 0.99 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file23117fa45f92/annotations.parquet] > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3aab38e6/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file23117fa45f92/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file23117fa45f92] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23117fa45f92'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23117fa45f92'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.18 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-files.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3aab38e6/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3aab38e6] > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3aab38e6'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3aab38e6'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.38 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 0.97 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 0.98 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/ops/v001] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/ops/v001'] > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f37f1bdce/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-files.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f37f1bdce/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f37f1bdce] > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f37f1bdce'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f37f1bdce'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.38 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311392b96b8/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311392b96b8/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311392b96b8] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311392b96b8'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311392b96b8'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.2 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230fe35f8f3/annotations.parquet] > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230fe35f8f3/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230fe35f8f3] > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230fe35f8f3'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230fe35f8f3'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.38 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.02 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file231188d6e28/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file231188d6e28/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file231188d6e28] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231188d6e28'] > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231188d6e28'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.18 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.14 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.02 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.2 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 0.98 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_2311419e21fb/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_2311419e21fb/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_2311419e21fb] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_2311419e21fb'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_2311419e21fb'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 12.91 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f57d14d9b/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f57d14d9b/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f57d14d9b] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f57d14d9b'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f57d14d9b'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 15.22 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6259bc67/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6259bc67/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6259bc67] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6259bc67'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6259bc67'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 2.16 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f3e871302.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f323ee27b/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f323ee27b/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f323ee27b] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f323ee27b'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f323ee27b'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.08 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f20ec914b.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1c7e31a2/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1c7e31a2/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1c7e31a2] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1c7e31a2'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1c7e31a2'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.08 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. > test-io-repertoires-schema-table.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 1.15 secs > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23114504acbf/annotations.parquet] > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23114504acbf/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23114504acbf] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23114504acbf'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23114504acbf'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 12.93 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /Volumes/Temp/tmp/RtmpZg4BKT/file2311644c5e21.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23111beb0bb0/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23111beb0bb0/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23111beb0bb0] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23111beb0bb0'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23111beb0bb0'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 0.3 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /Volumes/Temp/tmp/RtmpZg4BKT/file23115e5458a7.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_231178b98ee4/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_231178b98ee4/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_231178b98ee4] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_231178b98ee4'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_231178b98ee4'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 0.33 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-agg-stepwise.R:125:3'): agg_repertoires single-chain stepwise materialized path is stable ── <duckdb_error/rlang_error/error/condition> Error in `(function (context, message, error_type = NULL, raw_message = NULL, extra_info = NULL) { fields <- list() fields$context <- context fields$error_type <- error_type fields$raw_message <- raw_message fields$extra_info <- extra_info error_parts <- c(message, i = paste0("Context: ", context)) if (!is.null(error_type)) { error_parts <- c(error_parts, i = paste0("Error type: ", error_type)) } if (length(extra_info) > 0) { info_text <- paste0(names(extra_info), ": ", extra_info) names(info_text) <- rep_len("i", length(info_text)) error_parts <- c(error_parts, info_text) } rlang::abort(error_parts, class = "duckdb_error", !!!fields) })("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n0 duckdb::Exception::Exception(duckdb::ExceptionType, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) + 52\n1 duckdb::InternalException::InternalException(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) + 20\n2 duckdb::InternalException::InternalException<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned long long&, unsigned long long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned long long&, unsigned long long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&&) + 136\n3 duckdb::ColumnBindingResolver::VisitReplace(duckdb::BoundColumnRefExpression&, duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*) + 616\n4 duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*) + 476\n5 duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::__1::function<void (duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)> const&) + 1148\n6 duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&) + 68\n7 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1972\n8 duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n9 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n10 duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n11 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n12 duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n13 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n14 duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long long, true, std::__1::allocator<unsigned long long>>&) + 84\n15 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n16 duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n17 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n18 duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n19 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n20 duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>) + 136\n21 duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>) + 48\n22 duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters) + 1376\n23 duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode) + 800\n24 duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&) + 128\n25 duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&) + 272\n26 duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&) + 1840\n27 duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool) + 220\n28 duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters) + 588\n29 duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&) + 132\n30 duckdb::Relation::Execute() + 124\n31 duckdb::AltrepRelationWrapper::Materialize() + 292\n32 duckdb::AltrepRelationWrapper::GetQueryResult() + 692\n33 RelToAltrep::RownamesLength(SEXPREC*) + 104\n34 do_shortRowNames + 292\n35 bcEval_loop + 20580\n36 bcEval + 628\n37 Rf_eval + 356\n38 R_execClosure + 796\n39 applyClosure_core + 164\n40 Rf_applyClosure + 12\n41 dispatchMethod + 1236\n42 Rf_usemethod + 520\n43 Rf_DispatchOrEval + 888\n44 do_dim + 112\n45 bcEval_loop + 20580\n46 bcEval + 628\n47 Rf_eval + 356\n48 R_execClosure + 796\n49 applyClosure_core + 164\n50 Rf_applyClosure + 12\n51 dispatchMethod + 1236\n52 Rf_usemethod + 764\n53 do_usemethod + 600\n54 bcEval_loop + 30772\n55 bcEval + 628\n56 Rf_eval + 356\n57 R_execClosure + 796\n58 applyClosure_core + 164\n59 Rf_applyClosure + 12\n60 dispatchMethod + 1236\n61 Rf_usemethod + 764\n62 do_usemethod + 600\n63 bcEval_loop + 30772\n64 bcEval + 628\n65 Rf_eval + 356\n66 R_execClosure + 796\n67 applyClosure_core + 164\n68 Rf_eval + 1640\n69 do_set + 356\n70 Rf_eval + 1024\n71 do_begin + 404\n72 Rf_eval + 1024\n73 do_eval + 1340\n74 bcEval_loop + 20580\n75 bcEval + 628\n76 Rf_eval + 356\n77 R_execClosure + 796\n78 applyClosure_core + 164\n79 Rf_eval + 1640\n80 do_eval + 1928\n81 bcEval_loop + 20580\n82 bcEval + 628\n83 Rf_eval + 356\n84 R_execClosure + 796\n85 applyClosure_core + 164\n86 Rf_eval + 1640\n87 do_begin + 404\n88 Rf_eval + 1024\n89 R_execClosure + 796\n90 applyClosure_core + 164\n91 Rf_eval + 1640\n92 do_docall + 628\n93 bcEval_loop + 20580\n94 bcEval + 628\n95 Rf_eval + 356\n96 R_execClosure + 796\n97 applyClosure_core + 164\n98 Rf_eval + 1640\n99 do_docall + 628\n100 bcEval_loop + 20580\n101 bcEval + 628\n102 Rf_eval + 356\n103 R_execClosure + 796\n104 applyClosure_core + 164\n105 Rf_eval + 1640\n106 forcePromise + 248\n107 getvar + 412\n108 bcEval_loop + 42712\n109 bcEval + 628\n110 Rf_eval + 356\n111 R_execClosure + 796\n112 applyClosure_core + 164\n113 Rf_eval + 1640\n114 do_begin + 404\n115 Rf_eval + 1024\n116 forcePromise + 248\n117 getvar + 412\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors")`: Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference "imd_barcode" [42.0]: inequal types (VARCHAR != INTEGER) Stack Trace: 0 duckdb::Exception::Exception(duckdb::ExceptionType, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) + 52 1 duckdb::InternalException::InternalException(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) + 20 2 duckdb::InternalException::InternalException<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned long long&, unsigned long long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned long long&, unsigned long long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&&) + 136 3 duckdb::ColumnBindingResolver::VisitReplace(duckdb::BoundColumnRefExpression&, duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*) + 616 4 duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*) + 476 5 duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::__1::function<void (duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)> const&) + 1148 6 duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&) + 68 7 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1972 8 duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108 9 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960 10 duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108 11 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960 12 duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108 13 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960 14 duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long long, true, std::__1::allocator<unsigned long long>>&) + 84 15 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960 16 duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108 17 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960 18 duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108 19 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960 20 duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>) + 136 21 duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>) + 48 22 duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters) + 1376 23 duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode) + 800 24 duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&) + 128 25 duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&) + 272 26 duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&) + 1840 27 duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool) + 220 28 duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters) + 588 29 duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&) + 132 30 duckdb::Relation::Execute() + 124 31 duckdb::AltrepRelationWrapper::Materialize() + 292 32 duckdb::AltrepRelationWrapper::GetQueryResult() + 692 33 RelToAltrep::RownamesLength(SEXPREC*) + 104 34 do_shortRowNames + 292 35 bcEval_loop + 20580 36 bcEval + 628 37 Rf_eval + 356 38 R_execClosure + 796 39 applyClosure_core + 164 40 Rf_applyClosure + 12 41 dispatchMethod + 1236 42 Rf_usemethod + 520 43 Rf_DispatchOrEval + 888 44 do_dim + 112 45 bcEval_loop + 20580 46 bcEval + 628 47 Rf_eval + 356 48 R_execClosure + 796 49 applyClosure_core + 164 50 Rf_applyClosure + 12 51 dispatchMethod + 1236 52 Rf_usemethod + 764 53 do_usemethod + 600 54 bcEval_loop + 30772 55 bcEval + 628 56 Rf_eval + 356 57 R_execClosure + 796 58 applyClosure_core + 164 59 Rf_applyClosure + 12 60 dispatchMethod + 1236 61 Rf_usemethod + 764 62 do_usemethod + 600 63 bcEval_loop + 30772 64 bcEval + 628 65 Rf_eval + 356 66 R_execClosure + 796 67 applyClosure_core + 164 68 Rf_eval + 1640 69 do_set + 356 70 Rf_eval + 1024 71 do_begin + 404 72 Rf_eval + 1024 73 do_eval + 1340 74 bcEval_loop + 20580 75 bcEval + 628 76 Rf_eval + 356 77 R_execClosure + 796 78 applyClosure_core + 164 79 Rf_eval + 1640 80 do_eval + 1928 81 bcEval_loop + 20580 82 bcEval + 628 83 Rf_eval + 356 84 R_execClosure + 796 85 applyClosure_core + 164 86 Rf_eval + 1640 87 do_begin + 404 88 Rf_eval + 1024 89 R_execClosure + 796 90 applyClosure_core + 164 91 Rf_eval + 1640 92 do_docall + 628 93 bcEval_loop + 20580 94 bcEval + 628 95 Rf_eval + 356 96 R_execClosure + 796 97 applyClosure_core + 164 98 Rf_eval + 1640 99 do_docall + 628 100 bcEval_loop + 20580 101 bcEval + 628 102 Rf_eval + 356 103 R_execClosure + 796 104 applyClosure_core + 164 105 Rf_eval + 1640 106 forcePromise + 248 107 getvar + 412 108 bcEval_loop + 42712 109 bcEval + 628 110 Rf_eval + 356 111 R_execClosure + 796 112 applyClosure_core + 164 113 Rf_eval + 1640 114 do_begin + 404 115 Rf_eval + 1024 116 forcePromise + 248 117 getvar + 412 This error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic. For more information, see https://duckdb.org/docs/stable/dev/internal_errors i Context: GetQueryResult Backtrace: ▆ 1. ├─dplyr::collect(single_chain_annotations) at test-io-repertoires-agg-stepwise.R:125:3 2. ├─duckplyr:::collect.prudent_duckplyr_df(single_chain_annotations) 3. │ ├─dplyr::collect(out) 4. │ └─duckplyr:::collect.duckplyr_df(out) 5. │ └─base::nrow(x) 6. │ ├─base::dim(x) 7. │ └─base::dim.data.frame(x) 8. │ └─base::.row_names_info(x, 2L) 9. └─duckdb (local) `<fn>`("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n0 duckdb::Exception::Exception(duckdb::ExceptionType, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) + 52\n1 duckdb::InternalException::InternalException(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) + 20\n2 duckdb::InternalException::InternalException<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned long long&, unsigned long long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned long long&, unsigned long long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&&) + 136\n3 duckdb::ColumnBindingResolver::VisitReplace(duckdb::BoundColumnRefExpression&, duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*) + 616\n4 duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*) + 476\n5 duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::__1::function<void (duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)> const&) + 1148\n6 duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&) + 68\n7 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1972\n8 duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n9 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n10 duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n11 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n12 duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n13 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n14 duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long long, true, std::__1::allocator<unsigned long long>>&) + 84\n15 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n16 duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n17 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n18 duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n19 duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n20 duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>) + 136\n21 duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>) + 48\n22 duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters) + 1376\n23 duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode) + 800\n24 duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&) + 128\n25 duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&) + 272\n26 duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&) + 1840\n27 duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool) + 220\n28 duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters) + 588\n29 duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&) + 132\n30 duckdb::Relation::Execute() + 124\n31 duckdb::AltrepRelationWrapper::Materialize() + 292\n32 duckdb::AltrepRelationWrapper::GetQueryResult() + 692\n33 RelToAltrep::RownamesLength(SEXPREC*) + 104\n34 do_shortRowNames + 292\n35 bcEval_loop + 20580\n36 bcEval + 628\n37 Rf_eval + 356\n38 R_execClosure + 796\n39 applyClosure_core + 164\n40 Rf_applyClosure + 12\n41 dispatchMethod + 1236\n42 Rf_usemethod + 520\n43 Rf_DispatchOrEval + 888\n44 do_dim + 112\n45 bcEval_loop + 20580\n46 bcEval + 628\n47 Rf_eval + 356\n48 R_execClosure + 796\n49 applyClosure_core + 164\n50 Rf_applyClosure + 12\n51 dispatchMethod + 1236\n52 Rf_usemethod + 764\n53 do_usemethod + 600\n54 bcEval_loop + 30772\n55 bcEval + 628\n56 Rf_eval + 356\n57 R_execClosure + 796\n58 applyClosure_core + 164\n59 Rf_applyClosure + 12\n60 dispatchMethod + 1236\n61 Rf_usemethod + 764\n62 do_usemethod + 600\n63 bcEval_loop + 30772\n64 bcEval + 628\n65 Rf_eval + 356\n66 R_execClosure + 796\n67 applyClosure_core + 164\n68 Rf_eval + 1640\n69 do_set + 356\n70 Rf_eval + 1024\n71 do_begin + 404\n72 Rf_eval + 1024\n73 do_eval + 1340\n74 bcEval_loop + 20580\n75 bcEval + 628\n76 Rf_eval + 356\n77 R_execClosure + 796\n78 applyClosure_core + 164\n79 Rf_eval + 1640\n80 do_eval + 1928\n81 bcEval_loop + 20580\n82 bcEval + 628\n83 Rf_eval + 356\n84 R_execClosure + 796\n85 applyClosure_core + 164\n86 Rf_eval + 1640\n87 do_begin + 404\n88 Rf_eval + 1024\n89 R_execClosure + 796\n90 applyClosure_core + 164\n91 Rf_eval + 1640\n92 do_docall + 628\n93 bcEval_loop + 20580\n94 bcEval + 628\n95 Rf_eval + 356\n96 R_execClosure + 796\n97 applyClosure_core + 164\n98 Rf_eval + 1640\n99 do_docall + 628\n100 bcEval_loop + 20580\n101 bcEval + 628\n102 Rf_eval + 356\n103 R_execClosure + 796\n104 applyClosure_core + 164\n105 Rf_eval + 1640\n106 forcePromise + 248\n107 getvar + 412\n108 bcEval_loop + 42712\n109 bcEval + 628\n110 Rf_eval + 356\n111 R_execClosure + 796\n112 applyClosure_core + 164\n113 Rf_eval + 1640\n114 do_begin + 404\n115 Rf_eval + 1024\n116 forcePromise + 248\n117 getvar + 412\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors") 10. └─rlang::abort(error_parts, class = "duckdb_error", !!!fields) ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:205:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:208:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:212:5 ── Failure ('test-io-repertoires-agg.R:62:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample1 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:68:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample2_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample2 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:86:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count1[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 ── Failure ('test-io-repertoires-agg.R:94:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count2[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ] Error: ! Test failures. Execution halted Flavor: r-devel-macos-arm64

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [451s/239s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5712a66cf81/annotations.parquet] > test-annotate-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5712a66cf81/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5712a66cf81] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5712a66cf81'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5712a66cf81'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 7.29 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7245de74/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7245de74/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7245de74] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7245de74'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7245de74'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 8.64 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e508ee606/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e508ee606/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e508ee606] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e508ee606'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e508ee606'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.23 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714cb2e5ab/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714cb2e5ab/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714cb2e5ab] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714cb2e5ab'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714cb2e5ab'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.9 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e58cc8347/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e58cc8347/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e58cc8347] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e58cc8347'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e58cc8347'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.16 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57133eda45f/annotations.parquet] > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57133eda45f/metadata.json] > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57133eda45f] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57133eda45f'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57133eda45f'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.57 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: 1. exclude_columns > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa0498f/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa0498f/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa0498f] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa0498f'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa0498f'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.69 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e51b1fad4/annotations.parquet] > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e51b1fad4/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e51b1fad4] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e51b1fad4'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e51b1fad4'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.5 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571514dbd21/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571514dbd21/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571514dbd21] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571514dbd21'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571514dbd21'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.7 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e5f07fbe8/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e5f07fbe8/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e5f07fbe8] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e5f07fbe8'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e5f07fbe8'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.4 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714876edc6/annotations.parquet] > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714876edc6/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714876edc6] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714876edc6'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714876edc6'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.72 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e77e9e1cd/annotations.parquet] > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716ea16b2a/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e77e9e1cd/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e77e9e1cd] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e77e9e1cd'] > test-annotate-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716ea16b2a/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716ea16b2a] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e77e9e1cd'] > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716ea16b2a'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.13 secs > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716ea16b2a'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: i Time elapsed: 4.75 secs > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57165843522/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57165843522/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57165843522] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57165843522'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57165843522'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 5.99 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FAL > test-compute-collect-immundata.R: SE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e83e6e8/annotations.parquet] > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e83e6e8/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e83e6e8] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e83e6e8'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e83e6e8'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.09 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57171aae9af/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57171aae9af/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57171aae9af] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57171aae9af'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57171aae9af'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.15 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Respons > test-compute-collect-immundata.R: e, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7812c511/annotations.parquet] > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7812c511/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7812c511] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7812c511'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7812c511'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.55 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f5c6296/annotations.parquet] > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f5c6296/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f5c6296] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f5c6296'] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f5c6296'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: i Time elapsed: 6.11 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e26ee64ef/annotations.parquet] > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e26ee64ef/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e26ee64ef] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e26ee64ef'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e26ee64ef'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.5 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711b0fbfe8/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711b0fbfe8/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711b0fbfe8] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711b0fbfe8'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711b0fbfe8'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 7.14 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e6ecb15c8/annotations.parquet] > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571703d7ebc/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e6ecb15c8/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e6ecb15c8] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e6ecb15c8'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e6ecb15c8'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.12 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571703d7ebc/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571703d7ebc] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571703d7ebc'] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571703d7ebc'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 4.78 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: 2. filter_nonproductive > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57161cbd50b/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-exact.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57161cbd50b/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57161cbd50b] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57161cbd50b'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57161cbd50b'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 4.77 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e1087349b/annotations.parquet] > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e1087349b/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e1087349b] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e1087349b'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e1087349b'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.16 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa3d70e/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa3d70e/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa3d70e] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa3d70e'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa3d70e'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 4.72 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7d62dd0c/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7d62dd0c/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7d62dd0c] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7d62dd0c'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7d62dd0c'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.26 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711e6fc74b/annotations.parquet] > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711e6fc74b/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711e6fc74b] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711e6fc74b'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711e6fc74b'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 4.8 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57119b57338/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e62c770d5/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57119b57338/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57119b57338] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57119b57338'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57119b57338'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 4.68 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e62c770d5/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e62c770d5] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e62c770d5'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e62c770d5'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.52 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571285fe46a/annotations.parquet] > test-filter-immundata-regex.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571285fe46a/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571285fe46a] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571285fe46a'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571285fe46a'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 4.72 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e4f311567/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e4f311567/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e4f311567] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e4f311567'] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e4f311567'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 6.13 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714f7c4b2f/annotations.parquet] > test-filter-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714f7c4b2f/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714f7c4b2f] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714f7c4b2f'] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714f7c4b2f'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 4.67 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e447ceb82/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e447ceb82/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e447ceb82] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e447ceb82'] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e447ceb82'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 4.69 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/legacy_v1_27e57170560ebd/annotations.parquet] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e16e7be.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/legacy_v1_27e57170560ebd/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/legacy_v1_27e57170560ebd] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/legacy_v1_27e57170560ebd'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/legacy_v1_27e57170560ebd'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.19 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/legacy_v1_27e57170560ebd'] > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e359a0cd0/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e359a0cd0/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e359a0cd0] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e359a0cd0'] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e359a0cd0'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.41 secs > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e395f3628.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e26f60e3e/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e26f60e3e/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e26f60e3e] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e26f60e3e'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e26f60e3e'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.39 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.19 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7c5a30b8.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6dcc4633/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6dcc4633/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6dcc4633] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6dcc4633'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6dcc4633'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.99 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.21 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e3a1213cb.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6da6e07/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.19 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6da6e07/metadata.json] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6da6e07] > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6da6e07'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6da6e07'] > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 2.18 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e220aa1b5.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e435451bb/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e435451bb/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e435451bb] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e435451bb'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e435451bb'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.79 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e741a6bca.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e402c82e2/annotations.parquet] > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e402c82e2/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e402c82e2] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e402c82e2'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e402c82e2'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.78 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e50154974.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-immundata.R: i Time elapsed: 5.12 secs > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-agg.R: 1. exclude_columns > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56edb726b1/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56edb726b1/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56edb726b1] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56edb726b1'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56edb726b1'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.89 secs > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.21 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e548ad262.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5f66cad7/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5f66cad7/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5f66cad7] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5f66cad7'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5f66cad7'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.48 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e2b40fcc2.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e11424709/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e11424709/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e11424709] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e11424709'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e11424709'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.43 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e3a93c26a.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.18 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/treated/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/treated/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/treated/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e63dcc282/annotations.parquet] > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e63dcc282/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e63dcc282] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e63dcc282'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e63dcc282'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.86 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56ebc0fe45.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e331b7826/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e331b7826/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e331b7826] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e331b7826'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e331b7826'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.38 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e5fece4f4.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.17 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32ddf55f/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32ddf55f/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32ddf55f] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32ddf55f'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32ddf55f'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.46 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e11604388.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.15 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e643fc9b/annotations.parquet] > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e643fc9b/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e643fc9b] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e643fc9b'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e643fc9b'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.22 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e143786ca.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e66842747/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e66842747/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e66842747] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e66842747'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e66842747'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.27 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e2434ce9.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e355eb090/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e355eb090/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e355eb090] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e355eb090'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e355eb090'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.96 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e2434ce9.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57126114b77/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e42b23417/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57126114b77/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57126114b77] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57126114b77'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57126114b77'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.72 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e42b23417/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e42b23417] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e42b23417'] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e42b23417'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.69 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.16 secs > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e3d95b89f/annotations.parquet] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e3d95b89f/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/snapshots/baseline/v001'] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e3d95b89f] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e3d95b89f'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e3d95b89f'] > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-immundata.R: v All files have the same extension > test-io-repertoires-files.R: i Time elapsed: 2.23 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: v Renaming is finished > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.14 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/ops/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/ops/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e13bd8c16/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e13bd8c16/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e13bd8c16] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e13bd8c16'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e13bd8c16'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 4.03 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57130bcd6b7/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57130bcd6b7/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57130bcd6b7] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57130bcd6b7'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57130bcd6b7'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.8 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e1cf933b/annotations.parquet] > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e1cf933b/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e1cf933b] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e1cf933b'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e1cf933b'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 4.03 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f7636fa/annotations.parquet] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f7636fa/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f7636fa] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f7636fa'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f7636fa'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.72 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b7f81d2/annotations.parquet > test-io-repertoires-files.R: ] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b7f81d2/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b7f81d2] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b7f81d2'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b7f81d2'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.17 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude/annotations.parquet] > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.29 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-rename/metadata.json] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-rename'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.64 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b5258c3/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b5258c3/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b5258c3] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b5258c3'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b5258c3'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.12 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude-rename/annotations.parquet] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.32 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e14bd5690/annotations.parquet] > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e14bd5690/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e14bd5690] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e14bd5690'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e14bd5690'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.59 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57137a436c2/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57137a436c2/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57137a436c2] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57137a436c2'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57137a436c2'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 25.46 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors Saving _problems/test-io-repertoires-processing-90.R Saving _problems/test-io-repertoires-processing-110.R > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56eb5b311b/annotations.parquet] > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e571323f179b/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e571323f179b/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e571323f179b] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e571323f179b'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e571323f179b'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 5.51 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56eb5b311b/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56eb5b311b] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56eb5b311b'] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56eb5b311b'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 31.46 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /home/hornik/tmp/scratch/RtmpQtwpxz/file27e57121ff23cb.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57151a8cfb7/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57151a8cfb7/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57151a8cfb7] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57151a8cfb7'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57151a8cfb7'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.37 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /home/hornik/tmp/scratch/RtmpQtwpxz/file27e571553cf8a0.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57156001248/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57156001248/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57156001248] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57156001248'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57156001248'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.39 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. > test-io-repertoires-schema-table.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 2.61 secs > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e49c2496e/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e49c2496e/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e49c2496e] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e49c2496e'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e49c2496e'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 32.14 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e4edff99f.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e392c0147/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e392c0147/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e392c0147] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e392c0147'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e392c0147'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.48 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e226e5641.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32498da2/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32498da2/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32498da2] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32498da2'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32498da2'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.57 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 2 | WARN 0 | SKIP 0 | PASS 349 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-processing.R:87:3'): read_repertoires() removes non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:87:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires-processing.R:106:3'): read_repertoires() correctly reads non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:106:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 349 ] Error: ! Test failures. Execution halted Flavor: r-patched-linux-x86_64

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [468s/248s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566051ee6a698/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566051ee6a698/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566051ee6a698] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566051ee6a698'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566051ee6a698'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 6.15 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/file3566124be2963a/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/file3566124be2963a/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/file3566124be2963a] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file3566124be2963a'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file3566124be2963a'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 7.51 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/file35661279003789/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/file35661279003789/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/file35661279003789] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file35661279003789'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file35661279003789'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.46 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605962d304/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605962d304/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605962d304] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file356605962d304'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file356605962d304'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 5.16 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612699e432a/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612699e432a/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612699e432a] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612699e432a'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612699e432a'] > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.24 secs > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605754aef7f/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605754aef7f/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605754aef7f] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file356605754aef7f'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file356605754aef7f'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.81 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566056be2e66a/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566056be2e66a/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566056be2e66a] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566056be2e66a'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566056be2e66a'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.77 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/file3566121b7fcfc/annotations.parquet] > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/file3566121b7fcfc/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/file3566121b7fcfc] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file3566121b7fcfc'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file3566121b7fcfc'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.18 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566057002dec6/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566057002dec6/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566057002dec6] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566057002dec6'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566057002dec6'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 5.08 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612107b67cf/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612107b67cf/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612107b67cf] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612107b67cf'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612107b67cf'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.73 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566055db70e6f/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566055db70e6f/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566055db70e6f] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566055db70e6f'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566055db70e6f'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 5.29 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612193bdb80/annotations.parquet] > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file35660535b7f42d/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612193bdb80/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612193bdb80] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612193bdb80'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612193bdb80'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.91 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file35660535b7f42d/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file35660535b7f42d] > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file35660535b7f42d'] > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file35660535b7f42d'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 5.43 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566055b4c9840/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566055b4c9840/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566055b4c9840] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566055b4c9840'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566055b4c9840'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.11 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/file3566126a6a1ae9/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/file3566126a6a1ae9/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/file3566126a6a1ae9] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file3566126a6a1ae9'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file3566126a6a1ae9'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.24 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file35660565fe31e6/annotations.parquet] > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file35660565fe31e6/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file35660565fe31e6] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file35660565fe31e6'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file35660565fe31e6'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.3 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Respons > test-compute-collect-immundata.R: e, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612564453fa/annotations.parquet] > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605681d2d7b/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612564453fa/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612564453fa] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612564453fa'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612564453fa'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.31 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605681d2d7b/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605681d2d7b] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file356605681d2d7b'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file356605681d2d7b'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.16 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612371b7129/annotations.parquet] > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566051a7dabf1/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612371b7129/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612371b7129] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612371b7129'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612371b7129'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.31 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566051a7dabf1/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566051a7dabf1] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566051a7dabf1'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566051a7dabf1'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.82 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-agg-strata.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: 2. filter_nonproductive > test-filter-barcodes.R: v Preprocessing plan is ready > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file35660541b79453/annotations.parquet] > test-filter-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file35660541b79453/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file35660541b79453] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file35660541b79453'] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file35660541b79453'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 4.83 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/file3566122361d656/annotations.parquet] > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/file3566122361d656/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/file3566122361d656] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file3566122361d656'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file3566122361d656'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.24 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566053581f9b/annotations.parquet] > test-filter-immundata-exact.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566053581f9b/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566053581f9b] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566053581f9b'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566053581f9b'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 4.91 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/file35661256de097a/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/file35661256de097a/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/file35661256de097a] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file35661256de097a'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file35661256de097a'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.19 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605174e3d13/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605174e3d13/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605174e3d13] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file356605174e3d13'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file356605174e3d13'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 4.79 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612523c0786/annotations.parquet] > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file35660530cdbc41/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612523c0786/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612523c0786] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612523c0786'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612523c0786'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.35 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file35660530cdbc41/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file35660530cdbc41] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file35660530cdbc41'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file35660530cdbc41'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 4.87 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605456ff7af/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605456ff7af/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605456ff7af] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file356605456ff7af'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file356605456ff7af'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 4.78 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612517aa4ef/annotations.parquet] > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612517aa4ef/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612517aa4ef] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612517aa4ef'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612517aa4ef'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.14 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605615ea683/annotations.parquet] > test-filter-immundata-regex.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605615ea683/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605615ea683] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file356605615ea683'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file356605615ea683'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 4.82 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/file3566127ea0b451/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/file3566127ea0b451/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/file3566127ea0b451] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file3566127ea0b451'] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file3566127ea0b451'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 6.24 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566053a618037/annotations.parquet] > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566053a618037/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566053a618037] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566053a618037'] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566053a618037'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 4.86 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/legacy_v1_3566051a8dffc2/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/legacy_v1_3566051a8dffc2/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/legacy_v1_3566051a8dffc2] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/legacy_v1_3566051a8dffc2'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/legacy_v1_3566051a8dffc2'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.21 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/legacy_v1_3566051a8dffc2'] > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612618f4adc/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612618f4adc/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/file356612618f4adc] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612618f4adc'] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/file356612618f4adc'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 4.81 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file3566126b381aa7.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_356612728b5b26/annotations.parquet] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_356612728b5b26/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_356612728b5b26] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_356612728b5b26'] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_356612728b5b26'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.42 secs > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors Saving _problems/test-io-repertoires-agg-stepwise-125.R > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121f76fbba/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121f76fbba/metadata.json] > test-io-immundata.R: i Time elapsed: 2.21 secs > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121f76fbba] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121f76fbba'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121f76fbba'] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.48 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file35661224b6f4d9.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.24 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661220bfa2a/annotations.parquet] > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661220bfa2a/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661220bfa2a] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661220bfa2a'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661220bfa2a'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.61 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file35661268d1051a.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.23 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124137594b/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124137594b/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124137594b] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124137594b'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124137594b'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.61 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file3566123e8a0d1b.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661265ba029e/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661265ba029e/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661265ba029e] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661265ba029e'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661265ba029e'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.62 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file35661212d33725.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121020abec/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121020abec/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121020abec] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121020abec'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121020abec'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.63 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 5.29 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file3566125597041f.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-repertoires-agg.R: 1. exclude_columns > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661235556733/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661235556733/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661235556733] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661235556733'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661235556733'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.81 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.24 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-64.R Saving _problems/test-io-repertoires-agg-70.R Saving _problems/test-io-repertoires-agg-88.R Saving _problems/test-io-repertoires-agg-96.R > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file35661278ff4825.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661235ea0758/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661235ea0758/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661235ea0758] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661235ea0758'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661235ea0758'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.5 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file35661221628181.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121ba2d33d/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121ba2d33d/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121ba2d33d] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121ba2d33d'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121ba2d33d'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.48 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file3566124a8293e8.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.21 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/treated/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/treated/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/treated/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566126c24aa02/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566126c24aa02/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566126c24aa02] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566126c24aa02'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566126c24aa02'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.98 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file35661215fe5001.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.23 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121785ab0b/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121785ab0b/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121785ab0b] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121785ab0b'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121785ab0b'] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.64 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file35661242b9b0c8.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566123d614f70/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566123d614f70/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566123d614f70] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566123d614f70'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566123d614f70'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.6 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file35661261ae7b9f.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.25 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661216260dab/annotations.parquet] > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661216260dab/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661216260dab] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661216260dab'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661216260dab'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.78 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file35661252df2908.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_356612578259bb/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_356612578259bb/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_356612578259bb] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_356612578259bb'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_356612578259bb'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.24 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file3566122eb5148.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661237e0012c/annotations.parquet > test-io-repertoires-counts.R: ] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661237e0012c/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661237e0012c] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661237e0012c'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661237e0012c'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.48 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file3566122eb5148.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file35660568c2af67/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661267c62c8c/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file35660568c2af67/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file35660568c2af67] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file35660568c2af67'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file35660568c2af67'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.72 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661267c62c8c/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661267c62c8c] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661267c62c8c'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661267c62c8c'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.76 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_356612142ca0c7/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.22 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_356612142ca0c7/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_356612142ca0c7] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_356612142ca0c7'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_356612142ca0c7'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB/annotations.parquet] > test-io-repertoires-files.R: i Time elapsed: 2.29 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB/snapshots/baseline/v001/annotations.parquet] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectB/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.17 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/ops/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/imd_snap_tests/projectA/snapshots/ops/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124f062a62/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124f062a62/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124f062a62] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124f062a62'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124f062a62'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 4.19 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566055432c045/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566055432c045/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file3566055432c045] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566055432c045'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file3566055432c045'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.86 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124cd27309/annotations.parquet] > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124cd27309/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124cd27309] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124cd27309'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124cd27309'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 4.27 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605a28c33f/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605a28c33f/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/file356605a28c33f] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file356605a28c33f'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/file356605a28c33f'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.8 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124131b764/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124131b764/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124131b764] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124131b764'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566124131b764'] > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/test-exclude/annotations.parquet] > test-io-repertoires-files.R: i Time elapsed: 5.56 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/test-exclude/metadata.json] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.32 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.69 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121ef1edf1/annotations.parquet] > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/test-exclude-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.38 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121ef1edf1/metadata.json] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121ef1edf1] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121ef1edf1'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121ef1edf1'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.51 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566126ecd472a/annotations.parquet] > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566126ecd472a/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566126ecd472a] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566126ecd472a'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566126ecd472a'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.4 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_35660532453985/annotations.parquet > test-io-repertoires-processing.R: ] > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661245c25e33/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_35660532453985/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_35660532453985] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_35660532453985'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_35660532453985'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 35.66 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors Saving _problems/test-io-repertoires-processing-90.R Saving _problems/test-io-repertoires-processing-110.R > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661245c25e33/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661245c25e33] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661245c25e33'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661245c25e33'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 35.26 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_3566054493c604/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_3566054493c604/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_3566054493c604] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_3566054493c604'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_3566054493c604'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 5.54 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /home/hornik/tmp/scratch/RtmpY9DCn8/file3566056174af82.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_356605c29f494/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_356605c29f494/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_356605c29f494] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_356605c29f494'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_356605c29f494'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.39 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /home/hornik/tmp/scratch/RtmpY9DCn8/file356605f000b0b.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_3566051eb074d8/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_3566051eb074d8/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_3566051eb074d8] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_3566051eb074d8'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test_immundata_3566051eb074d8'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.42 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. > test-io-repertoires-schema-table.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpY9DCn8/test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpY9DCn8/test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpY9DCn8/test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpY9DCn8/test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 2.71 secs > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121ebbc478/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121ebbc478/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121ebbc478] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121ebbc478'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566121ebbc478'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 32.47 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file3566125a314b1d.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566126a27f77e/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566126a27f77e/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566126a27f77e] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566126a27f77e'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_3566126a27f77e'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.58 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /home/hornik/tmp/scratch/RtmpKgJLux/file35661229351460.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661264836291/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661264836291/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661264836291] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661264836291'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpKgJLux/test_immundata_35661264836291'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.71 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 10 | WARN 0 | SKIP 0 | PASS 314 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-agg-stepwise.R:125:3'): agg_repertoires single-chain stepwise materialized path is stable ── <duckdb_error/rlang_error/error/condition> Error in `(function (context, message, error_type = NULL, raw_message = NULL, extra_info = NULL) { fields <- list() fields$context <- context fields$error_type <- error_type fields$raw_message <- raw_message fields$extra_info <- extra_info error_parts <- c(message, i = paste0("Context: ", context)) if (!is.null(error_type)) { error_parts <- c(error_parts, i = paste0("Error type: ", error_type)) } if (length(extra_info) > 0) { info_text <- paste0(names(extra_info), ": ", extra_info) names(info_text) <- rep_len("i", length(info_text)) error_parts <- c(error_parts, info_text) } rlang::abort(error_parts, class = "duckdb_error", !!!fields) })("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::ToJSON(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x54) [0x7f8094c74254]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::Exception(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7f8094c74281]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7f8094c77251]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x199) [0x7f8094f7ed99]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(+0x90b5cb) [0x7f809410b5cb]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)+0x118) [0x7f8095838f28]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::function<void (duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)> const&)+0x7d) [0x7f809583ab8d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x3f) [0x7f809583b12f]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7e) [0x7f8094f6c96e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f809584b72d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f809584b72d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f809584b72d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::allocator<unsigned long> >&)+0x37) [0x7f80958475c7]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f809584b72d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f809584b72d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x8a) [0x7f8094f6d2fa]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x2a) [0x7f8094f6d4ea]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x685) [0x7f8095639775]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x4da) [0x7f8095639f1a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0xa6) [0x7f809563d026]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xa3) [0x7f809563d453]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0x8c) [0x7f809563d65c]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0x93) [0x7f809563e2f3]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x188) [0x7f8095641178]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x7d) [0x7f809564145d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x51) [0x7f8095641e21]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x137) [0x7f80943cb277]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x2b1) [0x7f80943cb971]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x45) [0x7f80943cc055]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0xa4515) [0x7f80b12a4515]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152869) [0x7f80b1352869]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c2f3) [0x7f80b139c2f3]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c867) [0x7f80b139c867]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x1565e0) [0x7f80b13565e0]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0xa7317) [0x7f80b12a7317]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152869) [0x7f80b1352869]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c2f3) [0x7f80b139c2f3]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c9e1) [0x7f80b139c9e1]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19cc1b) [0x7f80b139cc1b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x1434dc) [0x7f80b13434dc]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152869) [0x7f80b1352869]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c2f3) [0x7f80b139c2f3]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c9e1) [0x7f80b139c9e1]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19cc1b) [0x7f80b139cc1b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x1434dc) [0x7f80b13434dc]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15419d) [0x7f80b135419d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x52f) [0x7f80b134f31f]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152be4) [0x7f80b1352be4]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x52f) [0x7f80b134f31f]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x1555ef) [0x7f80b13555ef]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x155ab4) [0x7f80b1355ab4]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152be4) [0x7f80b1352be4]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x52f) [0x7f80b134f31f]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0xcba2e) [0x7f80b12cba2e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0xcba2e) [0x7f80b12cba2e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14f857) [0x7f80b134f857]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14fb65) [0x7f80b134fb65]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x147bed) [0x7f80b1347bed]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152be4) [0x7f80b1352be4]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x52f) [0x7f80b134f31f]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14f857) [0x7f80b134f857]\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors")`: Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference "imd_barcode" [42.0]: inequal types (VARCHAR != INTEGER) Stack Trace: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::ToJSON(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x54) [0x7f8094c74254] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::Exception(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7f8094c74281] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7f8094c77251] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x199) [0x7f8094f7ed99] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(+0x90b5cb) [0x7f809410b5cb] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)+0x118) [0x7f8095838f28] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::function<void (duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)> const&)+0x7d) [0x7f809583ab8d] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x3f) [0x7f809583b12f] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7e) [0x7f8094f6c96e] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f809584b72d] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f809584b72d] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f809584b72d] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::allocator<unsigned long> >&)+0x37) [0x7f80958475c7] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f809584b72d] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f809584b72d] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x8a) [0x7f8094f6d2fa] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x2a) [0x7f8094f6d4ea] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x685) [0x7f8095639775] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x4da) [0x7f8095639f1a] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0xa6) [0x7f809563d026] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xa3) [0x7f809563d453] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0x8c) [0x7f809563d65c] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0x93) [0x7f809563e2f3] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x188) [0x7f8095641178] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x7d) [0x7f809564145d] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x51) [0x7f8095641e21] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x137) [0x7f80943cb277] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x2b1) [0x7f80943cb971] /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x45) [0x7f80943cc055] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0xa4515) [0x7f80b12a4515] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152869) [0x7f80b1352869] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c2f3) [0x7f80b139c2f3] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c867) [0x7f80b139c867] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x1565e0) [0x7f80b13565e0] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0xa7317) [0x7f80b12a7317] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152869) [0x7f80b1352869] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c2f3) [0x7f80b139c2f3] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c9e1) [0x7f80b139c9e1] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19cc1b) [0x7f80b139cc1b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x1434dc) [0x7f80b13434dc] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152869) [0x7f80b1352869] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c2f3) [0x7f80b139c2f3] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c9e1) [0x7f80b139c9e1] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19cc1b) [0x7f80b139cc1b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x1434dc) [0x7f80b13434dc] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15419d) [0x7f80b135419d] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x52f) [0x7f80b134f31f] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152be4) [0x7f80b1352be4] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x52f) [0x7f80b134f31f] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x1555ef) [0x7f80b13555ef] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x155ab4) [0x7f80b1355ab4] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152be4) [0x7f80b1352be4] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x52f) [0x7f80b134f31f] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0xcba2e) [0x7f80b12cba2e] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0xcba2e) [0x7f80b12cba2e] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14f857) [0x7f80b134f857] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14fb65) [0x7f80b134fb65] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x147bed) [0x7f80b1347bed] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152be4) [0x7f80b1352be4] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x52f) [0x7f80b134f31f] /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14f857) [0x7f80b134f857] This error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic. For more information, see https://duckdb.org/docs/stable/dev/internal_errors i Context: GetQueryResult Backtrace: ▆ 1. ├─dplyr::collect(single_chain_annotations) at test-io-repertoires-agg-stepwise.R:125:3 2. ├─duckplyr:::collect.prudent_duckplyr_df(single_chain_annotations) 3. │ ├─dplyr::collect(out) 4. │ └─duckplyr:::collect.duckplyr_df(out) 5. │ └─base::nrow(x) 6. │ ├─base::dim(x) 7. │ └─base::dim.data.frame(x) 8. │ └─base::.row_names_info(x, 2L) 9. └─duckdb (local) `<fn>`("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::ToJSON(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x54) [0x7f8094c74254]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::Exception(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7f8094c74281]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7f8094c77251]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x199) [0x7f8094f7ed99]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(+0x90b5cb) [0x7f809410b5cb]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)+0x118) [0x7f8095838f28]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::function<void (duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)> const&)+0x7d) [0x7f809583ab8d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x3f) [0x7f809583b12f]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7e) [0x7f8094f6c96e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f809584b72d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f809584b72d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f809584b72d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::allocator<unsigned long> >&)+0x37) [0x7f80958475c7]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f809584b72d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f809584b72d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x73) [0x7f8094f6c963]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x8a) [0x7f8094f6d2fa]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x2a) [0x7f8094f6d4ea]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x685) [0x7f8095639775]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x4da) [0x7f8095639f1a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0xa6) [0x7f809563d026]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xa3) [0x7f809563d453]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0x8c) [0x7f809563d65c]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0x93) [0x7f809563e2f3]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x188) [0x7f8095641178]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x7d) [0x7f809564145d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x51) [0x7f8095641e21]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x137) [0x7f80943cb277]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x2b1) [0x7f80943cb971]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x45) [0x7f80943cc055]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0xa4515) [0x7f80b12a4515]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152869) [0x7f80b1352869]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c2f3) [0x7f80b139c2f3]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c867) [0x7f80b139c867]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x1565e0) [0x7f80b13565e0]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0xa7317) [0x7f80b12a7317]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152869) [0x7f80b1352869]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c2f3) [0x7f80b139c2f3]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c9e1) [0x7f80b139c9e1]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19cc1b) [0x7f80b139cc1b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x1434dc) [0x7f80b13434dc]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152869) [0x7f80b1352869]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c2f3) [0x7f80b139c2f3]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19c9e1) [0x7f80b139c9e1]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x19cc1b) [0x7f80b139cc1b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x1434dc) [0x7f80b13434dc]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15419d) [0x7f80b135419d]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x52f) [0x7f80b134f31f]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152be4) [0x7f80b1352be4]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x52f) [0x7f80b134f31f]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x1555ef) [0x7f80b13555ef]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x155ab4) [0x7f80b1355ab4]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152be4) [0x7f80b1352be4]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x52f) [0x7f80b134f31f]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0xcba2e) [0x7f80b12cba2e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0xcba2e) [0x7f80b12cba2e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x143705) [0x7f80b1343705]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14f857) [0x7f80b134f857]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14fb65) [0x7f80b134fb65]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x147bed) [0x7f80b1347bed]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14eb8b) [0x7f80b134eb8b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f80b134ef3b]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x15108e) [0x7f80b135108e]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x151e39) [0x7f80b1351e39]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f80b134f07a]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x152be4) [0x7f80b1352be4]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(Rf_eval+0x52f) [0x7f80b134f31f]\n/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libR.so(+0x14f857) [0x7f80b134f857]\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors") 10. └─rlang::abort(error_parts, class = "duckdb_error", !!!fields) ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:205:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:208:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /home/hornik/tmp/scratch/RtmpKgJLux/file35661254cce80b.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:212:5 ── Failure ('test-io-repertoires-agg.R:62:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample1 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:68:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample2_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample2 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:86:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count1[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 ── Failure ('test-io-repertoires-agg.R:94:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count2[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 ── Error ('test-io-repertoires-processing.R:87:3'): read_repertoires() removes non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:87:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires-processing.R:106:3'): read_repertoires() correctly reads non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:106:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) [ FAIL 10 | WARN 0 | SKIP 0 | PASS 314 ] Error: ! Test failures. Execution halted Flavor: r-release-linux-x86_64

Version: 0.0.6
Check: tests
Result: ERROR Running 'testthat.R' [256s] Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-barcodes.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c8ab6225/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c8ab6225/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c8ab6225] > test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c8ab6225'] > test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c8ab6225'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 5.44 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998462719b1/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998462719b1/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998462719b1] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998462719b1'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998462719b1'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.62 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899845f14036/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899845f14036/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899845f14036] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899845f14036'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899845f14036'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.56 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c84a1f3b/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c84a1f3b/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c84a1f3b] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c84a1f3b'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c84a1f3b'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 5.48 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998329d1e6/annotations.parquet] > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c480e4a8c/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998329d1e6/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998329d1e6] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998329d1e6'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998329d1e6'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.5 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c480e4a8c/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c480e4a8c] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c480e4a8c'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c480e4a8c'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 5.2 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c254b23ca/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c254b23ca/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c254b23ca] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c254b23ca'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c254b23ca'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 5.08 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998d360be/annotations.parquet] > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998d360be/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998d360be] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998d360be'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998d360be'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.73 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2edd5b6f/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2edd5b6f/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2edd5b6f] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2edd5b6f'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2edd5b6f'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 5.12 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89987afb7088/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89987afb7088/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89987afb7088] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89987afb7088'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89987afb7088'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.67 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c46a17b62/annotations.parquet] > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c46a17b62/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c46a17b62] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c46a17b62'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c46a17b62'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.96 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-receptors.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5ee946cf/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899821a65b70/annotations.parquet] > test-annotate-receptors.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5ee946cf/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5ee946cf] > test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5ee946cf'] > test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5ee946cf'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 4.92 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899821a65b70/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899821a65b70] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899821a65b70'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899821a65b70'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.3 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c20fa64b6/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c20fa64b6/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c20fa64b6] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c20fa64b6'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c20fa64b6'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.51 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89982c83782c/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89982c83782c/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89982c83782c] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89982c83782c'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89982c83782c'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.34 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c21d01e13/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c21d01e13/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c21d01e13] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c21d01e13'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c21d01e13'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.22 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-agg-strata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c72635e81/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984ca3e3b/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c72635e81/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c72635e81] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c72635e81'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c72635e81'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.15 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984ca3e3b/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984ca3e3b] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984ca3e3b'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984ca3e3b'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.27 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2791fd6/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2791fd6/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2791fd6] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2791fd6'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2791fd6'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.32 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-agg-strata.R: 1. prefix_barcodes > test-filter-barcodes.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-barcodes.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984b06b9d/annotations.parquet] > test-filter-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984b06b9d/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984b06b9d] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984b06b9d'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984b06b9d'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.42 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c36d94b09/annotations.parquet] > test-filter-barcodes.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c36d94b09/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c36d94b09] > test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c36d94b09'] > test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c36d94b09'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 5.12 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-exact.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899848ab5b62/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899848ab5b62/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899848ab5b62] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899848ab5b62'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899848ab5b62'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.54 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c1bd23cc7/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c1bd23cc7/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c1bd23cc7] > test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c1bd23cc7'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c1bd23cc7'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 5.13 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998205b4a42/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998205b4a42/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998205b4a42] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998205b4a42'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998205b4a42'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.55 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c76e01e70/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c76e01e70/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c76e01e70] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c76e01e70'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c76e01e70'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 4.91 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-lev.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5de52e31/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5de52e31/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5de52e31] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5de52e31'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5de52e31'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 5.17 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872206e69/annotations.parquet] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-lev.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872206e69/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872206e69] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872206e69'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872206e69'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.32 secs > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5f232b59/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5f232b59/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5f232b59] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5f232b59'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5f232b59'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 5.15 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-regex.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899869056fd6/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899869056fd6/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899869056fd6] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899869056fd6'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899869056fd6'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.77 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c39a9dea/annotations.parquet] > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c39a9dea/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c39a9dea] > test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c39a9dea'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c39a9dea'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 4.51 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-receptors.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872134e4a/annotations.parquet] > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c6d22e7/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872134e4a/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872134e4a] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872134e4a'] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872134e4a'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 6.4 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-receptors.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c6d22e7/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c6d22e7] > test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c6d22e7'] > test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c6d22e7'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 5.07 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\legacy_v1_c35c23e13e4a/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\legacy_v1_c35c23e13e4a/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\legacy_v1_c35c23e13e4a] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\legacy_v1_c35c23e13e4a'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\legacy_v1_c35c23e13e4a'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.08 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\legacy_v1_c35c23e13e4a'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998502f69e/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.18 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-filter-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998502f69e/metadata.json] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998502f69e] > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998502f69e'] > test-io-immundata.R: v All files have the same extension > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998502f69e'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 4.95 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899853667a8e.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981bce5121/annotations.parquet] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981bce5121/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981bce5121] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981bce5121'] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981bce5121'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.52 secs > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors Saving _problems/test-io-repertoires-agg-stepwise-125.R > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89986e491b03.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982e9e25ee/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982e9e25ee/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982e9e25ee] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982e9e25ee'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982e9e25ee'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.52 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.29 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998325a1c69.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.82 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d4012ec/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d4012ec/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d4012ec] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d4012ec'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d4012ec'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 2.36 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89983bcc170f.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899843625b07/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899843625b07/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899843625b07] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899843625b07'] > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899843625b07'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 2.65 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899816365064.tsv > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.97 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983d6177/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.05 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002'] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983d6177/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983d6177] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983d6177'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983d6177'] > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 2.46 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899813ad46f6.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.93 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\treated\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\treated\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\treated\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\treated\v001'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899817d34197/annotations.parquet] > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899817d34197/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899817d34197] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899817d34197'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899817d34197'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 2.37 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998bd650a0.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-repertoires-agg.R: 1. exclude_columns > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.2 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987cb263b7/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987cb263b7/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987cb263b7] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987cb263b7'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987cb263b7'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 2.36 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-64.R Saving _problems/test-io-repertoires-agg-70.R Saving _problems/test-io-repertoires-agg-88.R Saving _problems/test-io-repertoires-agg-96.R > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998655a686f.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.01 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981da24eba/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981da24eba/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981da24eba] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981da24eba'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981da24eba'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.55 secs > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998d8c7465.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899845025be1/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899845025be1/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899845025be1] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899845025be1'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899845025be1'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.54 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89987b449c2.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899870d420a0/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899870d420a0/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899870d420a0] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899870d420a0'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899870d420a0'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.16 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998696d8b2.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2db2656e/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899823e45d9f/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2db2656e/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2db2656e] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2db2656e'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2db2656e'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.85 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899823e45d9f/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899823e45d9f] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899823e45d9f'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899823e45d9f'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: i Time elapsed: 2.08 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89983e73671a.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899844032725/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.85 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB\snapshots\baseline\v001] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899844032725/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899844032725] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB\snapshots\baseline\v001'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899844032725'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899844032725'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-counts.R: i Time elapsed: 2.11 secs > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984843548e.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987585f7f/annotations.parquet] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.52 secs > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987585f7f/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987585f7f] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987585f7f'] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987585f7f'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.4 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\ops\v001/annotations.parquet] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89983c673350.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\ops\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\ops\v001] > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\ops\v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984fe41920/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984fe41920/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984fe41920] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984fe41920'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984fe41920'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.3 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89986ab36b31.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-repertoires-counts.R: v All files have the same extension > test-io-immundata.R: 1. exclude_columns > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998511295e/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998511295e/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998511295e] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998511295e'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998511295e'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.26 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89986ab36b31.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c66af48dd/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871cd5c3b/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c66af48dd/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c66af48dd] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c66af48dd'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c66af48dd'] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871cd5c3b/metadata.json] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 5.12 secs > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871cd5c3b] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871cd5c3b'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871cd5c3b'] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.59 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871252f07/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871252f07/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871252f07] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871252f07'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871252f07'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.27 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c52275d9e/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c52275d9e/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c52275d9e] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c52275d9e'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c52275d9e'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.87 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982af62e19/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982af62e19/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982af62e19] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982af62e19'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982af62e19'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.98 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.21 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d7e309a/annotations.parquet] > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.72 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d7e309a/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d7e309a] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d7e309a'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d7e309a'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.84 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.18 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.96 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984466fe2/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984466fe2/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984466fe2] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984466fe2'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984466fe2'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.45 secs > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.29 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899837e43df4/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899837e43df4/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899837e43df4] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899837e43df4'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899837e43df4'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.25 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998118276f1/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998118276f1/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998118276f1] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998118276f1'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998118276f1'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.23 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\ig\multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35cb184f96/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35cb184f96/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35cb184f96] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35cb184f96'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35cb184f96'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 32.99 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\ig\multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899857a677f8/annotations.parquet] > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c6e846e4/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c6e846e4/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c6e846e4] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c6e846e4'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c6e846e4'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 5.63 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c4fe1227b.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c58061958/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c58061958/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c58061958] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c58061958'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c58061958'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.44 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c232264c2.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c1e5aa24/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c1e5aa24/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c1e5aa24] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c1e5aa24'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c1e5aa24'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.42 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899857a677f8/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899857a677f8] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899857a677f8'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899857a677f8'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 34.61 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\ig\multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 2.52 secs > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899899220a6/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899899220a6/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899899220a6] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899899220a6'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899899220a6'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 34.09 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998589812da.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89985e222b0/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89985e222b0/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89985e222b0] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89985e222b0'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89985e222b0'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 2.33 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899865fe5857.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983ae75c81/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983ae75c81/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983ae75c81] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983ae75c81'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983ae75c81'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 2.32 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-agg-stepwise.R:125:3'): agg_repertoires single-chain stepwise materialized path is stable ── <duckdb_error/rlang_error/error/condition> Error in `(function (context, message, error_type = NULL, raw_message = NULL, extra_info = NULL) { fields <- list() fields$context <- context fields$error_type <- error_type fields$raw_message <- raw_message fields$extra_info <- extra_info error_parts <- c(message, i = paste0("Context: ", context)) if (!is.null(error_type)) { error_parts <- c(error_parts, i = paste0("Error type: ", error_type)) } if (length(extra_info) > 0) { info_text <- paste0(names(extra_info), ": ", extra_info) names(info_text) <- rep_len("i", length(info_text)) error_parts <- c(error_parts, info_text) } rlang::abort(error_parts, class = "duckdb_error", !!!fields) })("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors")`: Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference "imd_barcode" [42.0]: inequal types (VARCHAR != INTEGER) This error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic. For more information, see https://duckdb.org/docs/stable/dev/internal_errors i Context: GetQueryResult Backtrace: ▆ 1. ├─dplyr::collect(single_chain_annotations) at test-io-repertoires-agg-stepwise.R:125:3 2. ├─duckplyr:::collect.prudent_duckplyr_df(single_chain_annotations) 3. │ ├─dplyr::collect(out) 4. │ └─duckplyr:::collect.duckplyr_df(out) 5. │ └─base::nrow(x) 6. │ ├─base::dim(x) 7. │ └─base::dim.data.frame(x) 8. │ └─base::.row_names_info(x, 2L) 9. └─duckdb (local) `<fn>`("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors") 10. └─rlang::abort(error_parts, class = "duckdb_error", !!!fields) ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:205:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:208:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:212:5 ── Failure ('test-io-repertoires-agg.R:62:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample1 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:68:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample2_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample2 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:86:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count1[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 ── Failure ('test-io-repertoires-agg.R:94:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count2[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ] Error: ! Test failures. Execution halted Flavor: r-release-windows-x86_64

Version: 0.0.6
Check: Rd cross-references
Result: NOTE Unknown package ‘anndataR’ in Rd xrefs Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 0.0.6
Check: tests
Result: ERROR Running 'testthat.R' [346s] Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: Rows: 2 Columns: 4 > test-annotate-barcodes.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc2c62061/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc2c62061/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc2c62061] > test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc2c62061'] > test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc2c62061'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 7.49 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc48c91a58/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc48c91a58/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc48c91a58] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc48c91a58'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc48c91a58'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.37 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc7fc1218/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc7fc1218/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc7fc1218] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc7fc1218'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc7fc1218'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 8.76 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc22431ff0/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc22431ff0/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc22431ff0] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc22431ff0'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc22431ff0'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 6.9 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc68dde83/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc68dde83/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc68dde83] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc68dde83'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc68dde83'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 8.32 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc1b63190c/annotations.parquet] > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc1b63190c/metadata.json] > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc1b63190c] > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc1b63190c'] > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc1b63190c'] > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 6.73 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc2e506e31/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc2e506e31/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc2e506e31] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc2e506e31'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc2e506e31'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 6.44 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc2c98412c/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc2c98412c/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc2c98412c] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc2c98412c'] > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc2c98412c'] > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 8.61 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc5b696994/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc5b696994/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc5b696994] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc5b696994'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc5b696994'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 6.65 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc5f61774f/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc5f61774f/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc5f61774f] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc5f61774f'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc5f61774f'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 8.83 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc15e25f71/annotations.parquet] > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc15e25f71/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc15e25f71] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc15e25f71'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc15e25f71'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 6.57 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-receptors.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc7bee4726/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc2236e68/annotations.parquet] > test-annotate-receptors.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc7bee4726/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc7bee4726] > test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc7bee4726'] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc2236e68/metadata.json] > test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc7bee4726'] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc2236e68] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 6.64 secs > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc2236e68'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc2236e68'] > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i Time elapsed: 8.76 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc73992ff5/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc73992ff5/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc73992ff5] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc73992ff5'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc73992ff5'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 8.75 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc1f041f83/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc1f041f83/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc1f041f83] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc1f041f83'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc1f041f83'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.02 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc61606eae/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc61606eae/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc61606eae] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc61606eae'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc61606eae'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 9.36 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc62bb4879/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc64b53adf/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc62bb4879/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc62bb4879] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc62bb4879'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc62bb4879'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 8.69 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc64b53adf/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc64b53adf] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc64b53adf'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc64b53adf'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 8.81 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-compute-collect-immundata.R: v Joining plan is ready > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc5a297c09/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc5a297c09/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc5a297c09] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc5a297c09'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc5a297c09'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 8.73 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-barcodes.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc657b261d/annotations.parquet] > test-filter-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc657b261d/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc657b261d] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc657b261d'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc657b261d'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 8.76 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc7205aa6/annotations.parquet] > test-filter-barcodes.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc7205aa6/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc7205aa6] > test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc7205aa6'] > test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc7205aa6'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 6.27 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-exact.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc44134ec3/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc44134ec3/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc44134ec3] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc44134ec3'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc44134ec3'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 8.64 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffcb712e27/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffcb712e27/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffcb712e27] > test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffcb712e27'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffcb712e27'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 6.9 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc77a4134d/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc77a4134d/metadata.json] > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc77a4134d] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc77a4134d'] > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc77a4134d'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc534d5a3b/annotations.parquet] > test-agg-strata.R: i Time elapsed: 8.59 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc534d5a3b/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc534d5a3b] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc534d5a3b'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc534d5a3b'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 6.6 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-lev.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc1a3419ab/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc1a3419ab/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc1a3419ab] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc1a3419ab'] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc1a3419ab'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 6.62 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc6de839cc/annotations.parquet] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-lev.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc6de839cc/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc6de839cc] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc6de839cc'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc6de839cc'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 8.5 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc19af7c18/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc19af7c18/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc19af7c18] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc19af7c18'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc19af7c18'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 6.92 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-regex.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bccd99381c/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bccd99381c/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bccd99381c] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bccd99381c'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bccd99381c'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 8.67 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffcbfe10ed/annotations.parquet] > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffcbfe10ed/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffcbfe10ed] > test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffcbfe10ed'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffcbfe10ed'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 7.01 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-receptors.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc78a253d3/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc78a253d3/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc78a253d3] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc78a253d3'] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc78a253d3'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 8.24 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc22af45e8/annotations.parquet] > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-receptors.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc22af45e8/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc22af45e8] > test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc22af45e8'] > test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc22af45e8'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 6.59 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\legacy_v1_1bffc289e383c/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\legacy_v1_1bffc289e383c/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\legacy_v1_1bffc289e383c] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\legacy_v1_1bffc289e383c'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\legacy_v1_1bffc289e383c'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.8 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\legacy_v1_1bffc289e383c'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc42ba5797/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc42ba5797/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc42ba5797] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc42ba5797'] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc42ba5797'] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 7.06 secs > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/annotations.parquet] > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc3eba535f.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.21 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc79164a69/annotations.parquet] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc79164a69/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc79164a69] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc79164a69'] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc79164a69'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.81 secs > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors Saving _problems/test-io-repertoires-agg-stepwise-125.R > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc19dd2e0f.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc5bb42021/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc5bb42021/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc5bb42021] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc5bb42021'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc5bb42021'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.78 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.16 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc13bbeb0.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc161a6dad/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.1 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc161a6dad/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc161a6dad] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc161a6dad'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc161a6dad'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: i Time elapsed: 3.41 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc5a50d36.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc30584eed/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc30584eed/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc30584eed] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc30584eed'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc30584eed'] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-agg.R: i Time elapsed: 3.43 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc16f0336d.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 7.23 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc9d239e7/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc9d239e7/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc9d239e7] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc9d239e7'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc9d239e7'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 3.67 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc1ea6302a.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.14 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v002] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc442b2c83/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc442b2c83/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc442b2c83] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc442b2c83'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc442b2c83'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 3.43 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.86 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v002] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v002'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\treated\v001/annotations.parquet] > test-io-repertoires-agg.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc26ef17f2.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\treated\v001/metadata.json] > test-io-repertoires-agg.R: 1. exclude_columns > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\treated\v001] > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\treated\v001'] > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB'] > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc289b546d/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.75 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v002] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v002'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc289b546d/metadata.json] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc289b546d] > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc289b546d'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc289b546d'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 3.47 secs > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-64.R Saving _problems/test-io-repertoires-agg-70.R Saving _problems/test-io-repertoires-agg-88.R Saving _problems/test-io-repertoires-agg-96.R > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc1ec26e46.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc5b3d6d2d/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc5b3d6d2d/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc5b3d6d2d] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc5b3d6d2d'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc5b3d6d2d'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.73 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc5a287573.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcca5e4b2b/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcca5e4b2b/metadata.json] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcca5e4b2b] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcca5e4b2b'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcca5e4b2b'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.71 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc417720bb.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.97 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc7a901a7d/annotations.parquet] > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc7a901a7d/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc7a901a7d] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc7a901a7d'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc7a901a7d'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.93 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc63fd7f83.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc12d5a31/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc12d5a31/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc12d5a31] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc12d5a31'] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc12d5a31'] > test-io-immundata.R: 1. prefix_barcodes > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Time elapsed: 3.4 secs > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc23216a4/annotations.parquet] > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc30bb30c5.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc23216a4/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc23216a4] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc23216a4'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc23216a4'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 6.57 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc659a76ce/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc659a76ce/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc659a76ce] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc659a76ce'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc659a76ce'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 3.32 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc343020fd.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.89 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectB\snapshots\baseline\v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc2061750/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.7 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc2061750/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc2061750] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc2061750'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\ops\v001/annotations.parquet] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc2061750'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 3.7 secs > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\ops\v001/metadata.json] > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\ops\v001] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\imd_snap_tests\projectA\snapshots\ops\v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bccbcd6cd0.tsv > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-counts.R: v All files have the same extension > test-io-immundata.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc728b22c/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc728b22c/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc728b22c] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc728b22c'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc728b22c'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-repertoires-counts.R: i Time elapsed: 0.44 secs > test-io-immundata.R: 1. exclude_columns > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc5e185508.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc37c62586/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc37c62586/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc37c62586] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc37c62586'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc37c62586'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 3.33 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc5e185508.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc2cac4afa/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc2cac4afa/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc2cac4afa] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc2cac4afa'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc2cac4afa'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 6.42 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc820630/annotations.parquet] > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc820630/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc820630] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc820630'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc820630'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 3.65 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: v Renaming is finished > test-io-immundata.R: i No locus information found > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc74ef56f/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc74ef56f/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc74ef56f] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc74ef56f'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc74ef56f'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.1 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc3f9065f8/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc3f9065f8/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc3f9065f8] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc3f9065f8'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc3f9065f8'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 6.64 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc48696219/annotations.parquet] > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-exclude/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc48696219/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc48696219] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc48696219'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc48696219'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.14 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 3.05 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 3.33 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bccf6b217a/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bccf6b217a/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bccf6b217a] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bccf6b217a'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bccf6b217a'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.77 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-exclude-rename/annotations.parquet] > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 3.14 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: i Writing the metadata to [D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\immundata-sample_0_1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\immundata-sample_0_1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 4.02 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc6bbb282a/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc6bbb282a/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc6bbb282a] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc6bbb282a'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc6bbb282a'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 7.16 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: i Writing the metadata to [D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\immundata-sample_0_1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\immundata-sample_0_1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.66 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bccf415327/annotations.parquet] > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bccf415327/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bccf415327] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bccf415327'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bccf415327'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 7.14 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc190978eb/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc190978eb/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc190978eb] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc190978eb'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc190978eb'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 7.17 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\ig\multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc3cc6dbc/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc3cc6dbc/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc3cc6dbc] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc3cc6dbc'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc3cc6dbc'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 44.43 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\ig\multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc3e2e440c/annotations.parquet] > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc62d6204/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc62d6204/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc62d6204] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc62d6204'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc62d6204'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 7.58 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc691c7564.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc45783f3c/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc45783f3c/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc45783f3c] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc45783f3c'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc45783f3c'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.77 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\file1bffc23595625.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc1cf93dc5/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc1cf93dc5/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc1cf93dc5] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc1cf93dc5'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test_immundata_1bffc1cf93dc5'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.76 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc3e2e440c/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc3e2e440c] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc3e2e440c'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc3e2e440c'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 44.18 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\ig\multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\RtmpE5YFuG\test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 4.24 secs > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc2345fc1/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc2345fc1/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc2345fc1] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc2345fc1'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc2345fc1'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 45.2 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc56951d85.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc132e7636/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc132e7636/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc132e7636] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc132e7636'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc132e7636'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 2.74 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\file6bcc3a7c4350.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc1dbc7d1b/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc1dbc7d1b/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc1dbc7d1b] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc1dbc7d1b'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_27_17_37_41_8496\Rtmp8mqLtN\test_immundata_6bcc1dbc7d1b'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 3.14 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-agg-stepwise.R:125:3'): agg_repertoires single-chain stepwise materialized path is stable ── <duckdb_error/rlang_error/error/condition> Error in `(function (context, message, error_type = NULL, raw_message = NULL, extra_info = NULL) { fields <- list() fields$context <- context fields$error_type <- error_type fields$raw_message <- raw_message fields$extra_info <- extra_info error_parts <- c(message, i = paste0("Context: ", context)) if (!is.null(error_type)) { error_parts <- c(error_parts, i = paste0("Error type: ", error_type)) } if (length(extra_info) > 0) { info_text <- paste0(names(extra_info), ": ", extra_info) names(info_text) <- rep_len("i", length(info_text)) error_parts <- c(error_parts, info_text) } rlang::abort(error_parts, class = "duckdb_error", !!!fields) })("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors")`: Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference "imd_barcode" [42.0]: inequal types (VARCHAR != INTEGER) This error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic. For more information, see https://duckdb.org/docs/stable/dev/internal_errors i Context: GetQueryResult Backtrace: ▆ 1. ├─dplyr::collect(single_chain_annotations) at test-io-repertoires-agg-stepwise.R:125:3 2. ├─duckplyr:::collect.prudent_duckplyr_df(single_chain_annotations) 3. │ ├─dplyr::collect(out) 4. │ └─duckplyr:::collect.duckplyr_df(out) 5. │ └─base::nrow(x) 6. │ ├─base::dim(x) 7. │ └─base::dim.data.frame(x) 8. │ └─base::.row_names_info(x, 2L) 9. └─duckdb (local) `<fn>`("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors") 10. └─rlang::abort(error_parts, class = "duckdb_error", !!!fields) ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:205:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:208:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_27_17_37_41_8496\\Rtmp8mqLtN\\file6bcc19dd2e0f.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:212:5 ── Failure ('test-io-repertoires-agg.R:62:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample1 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:68:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample2_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample2 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:86:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count1[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 ── Failure ('test-io-repertoires-agg.R:94:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count2[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ] Error: ! Test failures. Execution halted Flavor: r-oldrel-windows-x86_64