Last updated on 2026-02-15 09:50:29 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.10.3 | 46.43 | 186.34 | 232.77 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.10.3 | 33.34 | 120.27 | 153.61 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.10.3 | 93.00 | 465.16 | 558.16 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.10.3 | 83.00 | 291.05 | 374.05 | ERROR | |
| r-devel-macos-arm64 | 0.10.3 | 12.00 | 62.00 | 74.00 | OK | |
| r-devel-windows-x86_64 | 0.10.3 | 49.00 | 188.00 | 237.00 | ERROR | |
| r-patched-linux-x86_64 | 0.10.3 | 48.61 | 162.41 | 211.02 | ERROR | |
| r-release-linux-x86_64 | 0.10.3 | 42.23 | 162.27 | 204.50 | ERROR | |
| r-release-macos-arm64 | 0.10.3 | OK | ||||
| r-release-macos-x86_64 | 0.10.3 | 31.00 | 236.00 | 267.00 | OK | |
| r-release-windows-x86_64 | 0.10.3 | 49.00 | 183.00 | 232.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.10.3 | NOTE | ||||
| r-oldrel-macos-x86_64 | 0.10.3 | 32.00 | 242.00 | 274.00 | NOTE | |
| r-oldrel-windows-x86_64 | 0.10.3 | 68.00 | 239.00 | 307.00 | ERROR |
Version: 0.10.3
Check: examples
Result: ERROR
Running examples in ‘immunarch-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: airr_public
> ### Title: Public indices - pairwise repertoire overlap
> ### Aliases: airr_public airr_public_intersection airr_public_jaccard
>
> ### ** Examples
>
> # Limit the number of threads used by the underlying DB for this session.
> # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
> db_exec("SET threads TO 1")
> # Load data
> immdata <- get_test_idata() |> agg_repertoires("Therapy")
Rows: 2 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): File, Therapy, Response, Prefix
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ℹ Found 2/2 repertoire files from the metadata on the disk
✔ Metadata parsed successfully
── Reading repertoire data
1.
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
2.
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
ℹ Checking if all files are of the same type
✔ All files have the same extension
── Renaming the columns and schemas
✔ Renaming is finished
── Preprocessing the data
1. exclude_columns
2. filter_nonproductive
✔ Preprocessing plan is ready
── Aggregating the data to receptors
ℹ No locus information found
ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
✔ Execution plan for receptor data aggregation and annotation is ready
── Joining the metadata table with the dataset using 'filename' column
✔ Joining plan is ready
── Postprocessing the data
1. prefix_barcodes
✔ Postprocessing plan is ready
── Saving the newly created ImmunData to disk
ℹ Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8xzWbI/file3a36f32cd14bb5/annotations.parquet]
ℹ Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8xzWbI/file3a36f32cd14bb5/metadata.json]
✔ ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8xzWbI/file3a36f32cd14bb5]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8xzWbI/file3a36f32cd14bb5']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8xzWbI/file3a36f32cd14bb5']
── Summary
ℹ Time elapsed: 9.87 secs
Error in `count()`:
! This operation cannot be carried out by DuckDB, and the input is a
stingy duckplyr frame.
ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and
continue with duckplyr.
ℹ See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ ├─dplyr::pull(count(idata), "n")
8. │ ├─dplyr::count(idata)
9. │ └─immundata:::count.ImmunData(idata)
10. │ ├─dplyr::count(x$annotations)
11. │ └─duckplyr:::count.duckplyr_df(x$annotations)
12. │ ├─duckplyr:::rel_try(...)
13. │ │ └─rlang::try_fetch(rel, error = identity)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─dplyr:::tally_n(...)
20. │ └─rlang::quo_is_null(wt)
21. └─rlang::abort(message = message)
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.10.3
Check: examples
Result: ERROR
Running examples in ‘immunarch-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: airr_public
> ### Title: Public indices - pairwise repertoire overlap
> ### Aliases: airr_public airr_public_intersection airr_public_jaccard
>
> ### ** Examples
>
> # Limit the number of threads used by the underlying DB for this session.
> # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
> db_exec("SET threads TO 1")
> # Load data
> immdata <- get_test_idata() |> agg_repertoires("Therapy")
Rows: 2 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): File, Therapy, Response, Prefix
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ℹ Found 2/2 repertoire files from the metadata on the disk
✔ Metadata parsed successfully
── Reading repertoire data
1.
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
2.
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
ℹ Checking if all files are of the same type
✔ All files have the same extension
── Renaming the columns and schemas
✔ Renaming is finished
── Preprocessing the data
1. exclude_columns
2. filter_nonproductive
✔ Preprocessing plan is ready
── Aggregating the data to receptors
ℹ No locus information found
ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
✔ Execution plan for receptor data aggregation and annotation is ready
── Joining the metadata table with the dataset using 'filename' column
✔ Joining plan is ready
── Postprocessing the data
1. prefix_barcodes
✔ Postprocessing plan is ready
── Saving the newly created ImmunData to disk
ℹ Writing the receptor annotation data to [/tmp/Rtmp0z5XT9/file1404695b25f711/annotations.parquet]
ℹ Writing the metadata to [/tmp/Rtmp0z5XT9/file1404695b25f711/metadata.json]
✔ ImmunData files saved to [/tmp/Rtmp0z5XT9/file1404695b25f711]
ℹ Reading ImmunData files from ['/tmp/Rtmp0z5XT9/file1404695b25f711']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['/tmp/Rtmp0z5XT9/file1404695b25f711']
── Summary
ℹ Time elapsed: 3.35 secs
Error in `count()`:
! This operation cannot be carried out by DuckDB, and the input is a
stingy duckplyr frame.
ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and
continue with duckplyr.
ℹ See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ ├─dplyr::pull(count(idata), "n")
8. │ ├─dplyr::count(idata)
9. │ └─immundata:::count.ImmunData(idata)
10. │ ├─dplyr::count(x$annotations)
11. │ └─duckplyr:::count.duckplyr_df(x$annotations)
12. │ ├─duckplyr:::rel_try(...)
13. │ │ └─rlang::try_fetch(rel, error = identity)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─dplyr:::tally_n(...)
20. │ └─rlang::quo_is_null(wt)
21. └─rlang::abort(message = message)
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.10.3
Check: examples
Result: ERROR
Running examples in ‘immunarch-Ex.R’ failed
The error most likely occurred in:
> ### Name: airr_public
> ### Title: Public indices - pairwise repertoire overlap
> ### Aliases: airr_public airr_public_intersection airr_public_jaccard
>
> ### ** Examples
>
> # Limit the number of threads used by the underlying DB for this session.
> # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
> db_exec("SET threads TO 1")
> # Load data
> immdata <- get_test_idata() |> agg_repertoires("Therapy")
Rows: 2 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): File, Therapy, Response, Prefix
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ℹ Found 2/2 repertoire files from the metadata on the disk
✔ Metadata parsed successfully
── Reading repertoire data
1. /data/gannet/ripley/R/test-dev/immundata/extdata/tsv/sample_0_1k.tsv
2. /data/gannet/ripley/R/test-dev/immundata/extdata/tsv/sample_1k_2k.tsv
ℹ Checking if all files are of the same type
✔ All files have the same extension
── Renaming the columns and schemas
✔ Renaming is finished
── Preprocessing the data
1. exclude_columns
2. filter_nonproductive
✔ Preprocessing plan is ready
── Aggregating the data to receptors
ℹ No locus information found
ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
✔ Execution plan for receptor data aggregation and annotation is ready
── Joining the metadata table with the dataset using 'filename' column
✔ Joining plan is ready
── Postprocessing the data
1. prefix_barcodes
✔ Postprocessing plan is ready
── Saving the newly created ImmunData to disk
ℹ Writing the receptor annotation data to [/tmp/RtmphBLuJs/working_dir/RtmpvzegJE/file30f37a71edc2a0/annotations.parquet]
ℹ Writing the metadata to [/tmp/RtmphBLuJs/working_dir/RtmpvzegJE/file30f37a71edc2a0/metadata.json]
✔ ImmunData files saved to [/tmp/RtmphBLuJs/working_dir/RtmpvzegJE/file30f37a71edc2a0]
ℹ Reading ImmunData files from ['/tmp/RtmphBLuJs/working_dir/RtmpvzegJE/file30f37a71edc2a0']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['/tmp/RtmphBLuJs/working_dir/RtmpvzegJE/file30f37a71edc2a0']
── Summary
ℹ Time elapsed: 19.99 secs
Error in `count()`:
! This operation cannot be carried out by DuckDB, and the input is a
stingy duckplyr frame.
ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and
continue with duckplyr.
ℹ See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ ├─dplyr::pull(count(idata), "n")
8. │ ├─dplyr::count(idata)
9. │ └─immundata:::count.ImmunData(idata)
10. │ ├─dplyr::count(x$annotations)
11. │ └─duckplyr:::count.duckplyr_df(x$annotations)
12. │ ├─duckplyr:::rel_try(...)
13. │ │ └─rlang::try_fetch(rel, error = identity)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─dplyr:::tally_n(...)
20. │ └─rlang::quo_is_null(wt)
21. └─rlang::abort(message = message)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.10.3
Check: examples
Result: ERROR
Running examples in 'immunarch-Ex.R' failed
The error most likely occurred in:
> ### Name: airr_public
> ### Title: Public indices - pairwise repertoire overlap
> ### Aliases: airr_public airr_public_intersection airr_public_jaccard
>
> ### ** Examples
>
> # Limit the number of threads used by the underlying DB for this session.
> # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
> db_exec("SET threads TO 1")
> # Load data
> immdata <- get_test_idata() |> agg_repertoires("Therapy")
Rows: 2 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): File, Therapy, Response, Prefix
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ℹ Found 2/2 repertoire files from the metadata on the disk
✔ Metadata parsed successfully
── Reading repertoire data
1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv
2. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_1k_2k.tsv
ℹ Checking if all files are of the same type
✔ All files have the same extension
── Renaming the columns and schemas
✔ Renaming is finished
── Preprocessing the data
1. exclude_columns
2. filter_nonproductive
✔ Preprocessing plan is ready
── Aggregating the data to receptors
ℹ No locus information found
ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
✔ Execution plan for receptor data aggregation and annotation is ready
── Joining the metadata table with the dataset using 'filename' column
✔ Joining plan is ready
── Postprocessing the data
1. prefix_barcodes
✔ Postprocessing plan is ready
── Saving the newly created ImmunData to disk
ℹ Writing the receptor annotation data to [D:\temp\2026_02_14_01_50_00_18536\RtmpQpspT7\file17d4c2e074c80/annotations.parquet]
ℹ Writing the metadata to [D:\temp\2026_02_14_01_50_00_18536\RtmpQpspT7\file17d4c2e074c80/metadata.json]
✔ ImmunData files saved to [D:\temp\2026_02_14_01_50_00_18536\RtmpQpspT7\file17d4c2e074c80]
ℹ Reading ImmunData files from ['D:\temp\2026_02_14_01_50_00_18536\RtmpQpspT7\file17d4c2e074c80']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['D:\temp\2026_02_14_01_50_00_18536\RtmpQpspT7\file17d4c2e074c80']
── Summary
ℹ Time elapsed: 4.73 secs
Error in `count()`:
! This operation cannot be carried out by DuckDB, and the input is a
stingy duckplyr frame.
ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and
continue with duckplyr.
ℹ See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ ├─dplyr::pull(count(idata), "n")
8. │ ├─dplyr::count(idata)
9. │ └─immundata:::count.ImmunData(idata)
10. │ ├─dplyr::count(x$annotations)
11. │ └─duckplyr:::count.duckplyr_df(x$annotations)
12. │ ├─duckplyr:::rel_try(...)
13. │ │ └─rlang::try_fetch(rel, error = identity)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─dplyr:::tally_n(...)
20. │ └─rlang::quo_is_null(wt)
21. └─rlang::abort(message = message)
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.10.3
Check: examples
Result: ERROR
Running examples in ‘immunarch-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: airr_public
> ### Title: Public indices - pairwise repertoire overlap
> ### Aliases: airr_public airr_public_intersection airr_public_jaccard
>
> ### ** Examples
>
> # Limit the number of threads used by the underlying DB for this session.
> # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
> db_exec("SET threads TO 1")
> # Load data
> immdata <- get_test_idata() |> agg_repertoires("Therapy")
Rows: 2 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): File, Therapy, Response, Prefix
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ℹ Found 2/2 repertoire files from the metadata on the disk
✔ Metadata parsed successfully
── Reading repertoire data
1.
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
2.
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
ℹ Checking if all files are of the same type
✔ All files have the same extension
── Renaming the columns and schemas
✔ Renaming is finished
── Preprocessing the data
1. exclude_columns
2. filter_nonproductive
✔ Preprocessing plan is ready
── Aggregating the data to receptors
ℹ No locus information found
ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
✔ Execution plan for receptor data aggregation and annotation is ready
── Joining the metadata table with the dataset using 'filename' column
✔ Joining plan is ready
── Postprocessing the data
1. prefix_barcodes
✔ Postprocessing plan is ready
── Saving the newly created ImmunData to disk
ℹ Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp9JXDXU/file3af1061bcccdcc/annotations.parquet]
ℹ Writing the metadata to [/home/hornik/tmp/scratch/Rtmp9JXDXU/file3af1061bcccdcc/metadata.json]
✔ ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp9JXDXU/file3af1061bcccdcc]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp9JXDXU/file3af1061bcccdcc']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp9JXDXU/file3af1061bcccdcc']
── Summary
ℹ Time elapsed: 6.98 secs
Error in `count()`:
! This operation cannot be carried out by DuckDB, and the input is a
stingy duckplyr frame.
ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and
continue with duckplyr.
ℹ See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ ├─dplyr::pull(count(idata), "n")
8. │ ├─dplyr::count(idata)
9. │ └─immundata:::count.ImmunData(idata)
10. │ ├─dplyr::count(x$annotations)
11. │ └─duckplyr:::count.duckplyr_df(x$annotations)
12. │ ├─duckplyr:::rel_try(...)
13. │ │ └─rlang::try_fetch(rel, error = identity)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─dplyr:::tally_n(...)
20. │ └─rlang::quo_is_null(wt)
21. └─rlang::abort(message = message)
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.10.3
Check: examples
Result: ERROR
Running examples in ‘immunarch-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: airr_public
> ### Title: Public indices - pairwise repertoire overlap
> ### Aliases: airr_public airr_public_intersection airr_public_jaccard
>
> ### ** Examples
>
> # Limit the number of threads used by the underlying DB for this session.
> # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
> db_exec("SET threads TO 1")
> # Load data
> immdata <- get_test_idata() |> agg_repertoires("Therapy")
Rows: 2 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): File, Therapy, Response, Prefix
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ℹ Found 2/2 repertoire files from the metadata on the disk
✔ Metadata parsed successfully
── Reading repertoire data
1.
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
2.
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
ℹ Checking if all files are of the same type
✔ All files have the same extension
── Renaming the columns and schemas
✔ Renaming is finished
── Preprocessing the data
1. exclude_columns
2. filter_nonproductive
✔ Preprocessing plan is ready
── Aggregating the data to receptors
ℹ No locus information found
ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
✔ Execution plan for receptor data aggregation and annotation is ready
── Joining the metadata table with the dataset using 'filename' column
✔ Joining plan is ready
── Postprocessing the data
1. prefix_barcodes
✔ Postprocessing plan is ready
── Saving the newly created ImmunData to disk
ℹ Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpk8moZN/file3495fe69b1a79c/annotations.parquet]
ℹ Writing the metadata to [/home/hornik/tmp/scratch/Rtmpk8moZN/file3495fe69b1a79c/metadata.json]
✔ ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpk8moZN/file3495fe69b1a79c]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpk8moZN/file3495fe69b1a79c']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpk8moZN/file3495fe69b1a79c']
── Summary
ℹ Time elapsed: 5.61 secs
Error in `count()`:
! This operation cannot be carried out by DuckDB, and the input is a
stingy duckplyr frame.
ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and
continue with duckplyr.
ℹ See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ ├─dplyr::pull(count(idata), "n")
8. │ ├─dplyr::count(idata)
9. │ └─immundata:::count.ImmunData(idata)
10. │ ├─dplyr::count(x$annotations)
11. │ └─duckplyr:::count.duckplyr_df(x$annotations)
12. │ ├─duckplyr:::rel_try(...)
13. │ │ └─rlang::try_fetch(rel, error = identity)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─dplyr:::tally_n(...)
20. │ └─rlang::quo_is_null(wt)
21. └─rlang::abort(message = message)
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.10.3
Check: examples
Result: ERROR
Running examples in 'immunarch-Ex.R' failed
The error most likely occurred in:
> ### Name: airr_public
> ### Title: Public indices - pairwise repertoire overlap
> ### Aliases: airr_public airr_public_intersection airr_public_jaccard
>
> ### ** Examples
>
> # Limit the number of threads used by the underlying DB for this session.
> # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
> db_exec("SET threads TO 1")
> # Load data
> immdata <- get_test_idata() |> agg_repertoires("Therapy")
Rows: 2 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): File, Therapy, Response, Prefix
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ℹ Found 2/2 repertoire files from the metadata on the disk
✔ Metadata parsed successfully
── Reading repertoire data
1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv
2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv
ℹ Checking if all files are of the same type
✔ All files have the same extension
── Renaming the columns and schemas
✔ Renaming is finished
── Preprocessing the data
1. exclude_columns
2. filter_nonproductive
✔ Preprocessing plan is ready
── Aggregating the data to receptors
ℹ No locus information found
ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
✔ Execution plan for receptor data aggregation and annotation is ready
── Joining the metadata table with the dataset using 'filename' column
✔ Joining plan is ready
── Postprocessing the data
1. prefix_barcodes
✔ Postprocessing plan is ready
── Saving the newly created ImmunData to disk
ℹ Writing the receptor annotation data to [D:\temp\2026_02_13_01_50_00_31302\Rtmp2JS96r\file6e785afc7a89/annotations.parquet]
ℹ Writing the metadata to [D:\temp\2026_02_13_01_50_00_31302\Rtmp2JS96r\file6e785afc7a89/metadata.json]
✔ ImmunData files saved to [D:\temp\2026_02_13_01_50_00_31302\Rtmp2JS96r\file6e785afc7a89]
ℹ Reading ImmunData files from ['D:\temp\2026_02_13_01_50_00_31302\Rtmp2JS96r\file6e785afc7a89']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['D:\temp\2026_02_13_01_50_00_31302\Rtmp2JS96r\file6e785afc7a89']
── Summary
ℹ Time elapsed: 5.36 secs
Error in `count()`:
! This operation cannot be carried out by DuckDB, and the input is a
stingy duckplyr frame.
ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and
continue with duckplyr.
ℹ See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ ├─dplyr::pull(count(idata), "n")
8. │ ├─dplyr::count(idata)
9. │ └─immundata:::count.ImmunData(idata)
10. │ ├─dplyr::count(x$annotations)
11. │ └─duckplyr:::count.duckplyr_df(x$annotations)
12. │ ├─duckplyr:::rel_try(...)
13. │ │ └─rlang::try_fetch(rel, error = identity)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─dplyr:::tally_n(...)
20. │ └─rlang::quo_is_null(wt)
21. └─rlang::abort(message = message)
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.10.3
Check: installed package size
Result: NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 2.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.10.3
Check: examples
Result: ERROR
Running examples in 'immunarch-Ex.R' failed
The error most likely occurred in:
> ### Name: airr_public
> ### Title: Public indices - pairwise repertoire overlap
> ### Aliases: airr_public airr_public_intersection airr_public_jaccard
>
> ### ** Examples
>
> # Limit the number of threads used by the underlying DB for this session.
> # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
> db_exec("SET threads TO 1")
> # Load data
> immdata <- get_test_idata() |> agg_repertoires("Therapy")
Rows: 2 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): File, Therapy, Response, Prefix
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ℹ Found 2/2 repertoire files from the metadata on the disk
✔ Metadata parsed successfully
── Reading repertoire data
1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv
2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv
ℹ Checking if all files are of the same type
✔ All files have the same extension
── Renaming the columns and schemas
✔ Renaming is finished
── Preprocessing the data
1. exclude_columns
2. filter_nonproductive
✔ Preprocessing plan is ready
── Aggregating the data to receptors
ℹ No locus information found
ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
✔ Execution plan for receptor data aggregation and annotation is ready
── Joining the metadata table with the dataset using 'filename' column
✔ Joining plan is ready
── Postprocessing the data
1. prefix_barcodes
✔ Postprocessing plan is ready
── Saving the newly created ImmunData to disk
ℹ Writing the receptor annotation data to [D:\temp\2026_02_13_01_50_00_31302\RtmpW6hg2b\file13b281bb02342/annotations.parquet]
ℹ Writing the metadata to [D:\temp\2026_02_13_01_50_00_31302\RtmpW6hg2b\file13b281bb02342/metadata.json]
✔ ImmunData files saved to [D:\temp\2026_02_13_01_50_00_31302\RtmpW6hg2b\file13b281bb02342]
ℹ Reading ImmunData files from ['D:\temp\2026_02_13_01_50_00_31302\RtmpW6hg2b\file13b281bb02342']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['D:\temp\2026_02_13_01_50_00_31302\RtmpW6hg2b\file13b281bb02342']
── Summary
ℹ Time elapsed: 6.78 secs
Error in `count()`:
! This operation cannot be carried out by DuckDB, and the input is a
stingy duckplyr frame.
ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and
continue with duckplyr.
ℹ See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ ├─dplyr::pull(count(idata), "n")
8. │ ├─dplyr::count(idata)
9. │ └─immundata:::count.ImmunData(idata)
10. │ ├─dplyr::count(x$annotations)
11. │ └─duckplyr:::count.duckplyr_df(x$annotations)
12. │ ├─duckplyr:::rel_try(...)
13. │ │ └─rlang::try_fetch(rel, error = identity)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─dplyr:::tally_n(...)
20. │ └─rlang::quo_is_null(wt)
21. └─rlang::abort(message = message)
Execution halted
Flavor: r-oldrel-windows-x86_64