Last updated on 2026-10-10 13:50:20 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.0.1 | 3.15 | 72.93 | 76.08 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.0.1 | 2.38 | 44.08 | 46.46 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.0.1 | 44.71 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.0.1 | 60.53 | ERROR | |||
| r-devel-windows-x86_64 | 0.0.1 | 6.00 | 111.00 | 117.00 | OK | |
| r-patched-linux-x86_64 | 0.0.1 | 3.94 | 77.20 | 81.14 | OK | |
| r-release-linux-x86_64 | 0.0.1 | OK | ||||
| r-release-macos-arm64 | 0.0.1 | 1.00 | 35.00 | 36.00 | OK | |
| r-release-macos-x86_64 | 0.0.1 | 2.00 | 162.00 | 164.00 | OK | |
| r-release-windows-x86_64 | 0.0.1 | 5.00 | 104.00 | 109.00 | OK | |
| r-oldrel-macos-arm64 | 0.0.1 | 1.00 | 33.00 | 34.00 | OK | |
| r-oldrel-macos-x86_64 | 0.0.1 | 3.00 | 180.00 | 183.00 | OK | |
| r-oldrel-windows-x86_64 | 0.0.1 | 6.00 | 126.00 | 132.00 | OK |
Version: 0.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [12s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(OdysseusCharacterizationModule)
>
> test_check("OdysseusCharacterizationModule")
attempting to download GiBleed
trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip'
Content type 'application/zip' length 6861852 bytes (6.5 MB)
==================================================
downloaded 6.5 MB
attempting to extract and load: /home/hornik/tmp/scratch/RtmpImOZ1a/GiBleed_5.3.zip to: /home/hornik/tmp/scratch/RtmpImOZ1a/GiBleed_5.3.sqlite
Saving _problems/test-covariateData-133.R
Connecting using SQLite driver
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpImOZ1a/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
Connecting using SQLite driver
Cohorts created in table main.cohort
▶ == Executing 1 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
✓ Complete: 1 succeeded, 0 failed out of 1
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpImOZ1a/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
Saving _problems/test-covariateData-323.R
Saving _problems/test-covariateData-328.R
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 2 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
• Executing spec 1002: Condition occurrence [-30, -1]
✓ 0 rows returned
✓ Complete: 2 succeeded, 0 failed out of 2
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 2 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
• Executing spec 9999: bad_spec
! Spec 9999 failed: Error executing SQL:
no such table: nonexistent_table_xyz
An error report has been created at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OdysseusCharacterizationModule.Rcheck/tests/testthat/errorReportSql.txt
✓ Complete: 1 succeeded, 1 failed out of 2
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 1 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
✓ Complete: 1 succeeded, 0 failed out of 1
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 0 analysis spec(s) ============================
✓ Complete: 0 succeeded, 0 failed out of 0
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 1 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
✓ Complete: 1 succeeded, 0 failed out of 1
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Visit occurrence [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Procedure occurrence [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Measurement [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Drug exposure [-365, -1]
✓ 0 rows returned
Saving _problems/test-executeSpec-integration-475.R
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 3 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
• Executing spec 2001: Drug exposure [-365, -1]
✓ 0 rows returned
• Executing spec 3001: Procedure occurrence [-365, -1]
✓ 0 rows returned
✓ Complete: 3 succeeded, 0 failed out of 3
Cohorts created in table main.cohort
Connecting using SQLite driver
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
Executing SQL took 0.00984 secs
✓ Created #concept_sets_c with 1 concept set(s): gi
• Executing spec 10301: Concept set: gi (Condition occurrence) [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 100101: Cohort: Celecoxib [-365, -1]
✓ 0 rows returned
Characterization Analysis Plan
========================================
Analysis Windows: 1
Base Feature Domains: 1 of 9 enabled
condition_occurrence
Cohort Features: disabled
Concept Set Features: disabled
Single Node Analysis Specifications
========================================
Total specs: 1
base : 1
First 5 analyses:
[1] Condition occurrence [-30, -1] (id=1001)
Single Node Spec
------------------------------
Analysis ID: 1001
Name: Condition occurrence [-30, -1]
Table: condition_occurrence
Window: [-30, -1]
Type: start
Overlap: FALSE
ATC: FALSE
Concept Set: FALSE
Aggregated: TRUE
Source: base
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 535 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-covariateData.R:133:3'): .assembleCovariateData produces empty CovariateData when no results ──
Error: not an error
Backtrace:
▆
1. └─Eunomia::getEunomiaConnectionDetails() at test-covariateData.R:133:3
2. └─Eunomia::getDatabaseFile(...)
3. └─Eunomia::extractLoadData(...)
4. └─Eunomia::loadDataFiles(...)
5. ├─DBI::dbExecute(conn = connection, statement = statement)
6. └─DBI::dbExecute(conn = connection, statement = statement)
7. ├─DBI::dbSendStatement(conn, statement, ...)
8. └─DBI::dbSendStatement(conn, statement, ...)
9. ├─DBI::dbSendQuery(conn, statement, ...)
10. └─RSQLite::dbSendQuery(conn, statement, ...)
11. └─RSQLite (local) .local(conn, statement, ...)
12. ├─methods::new(...)
13. │ ├─methods::initialize(value, ...)
14. │ └─methods::initialize(value, ...)
15. └─RSQLite:::result_create(conn@ptr, statement)
── Failure ('test-covariateData.R:323:3'): getDbOcmCovariateData produces valid CovariateData with Eunomia ──
Expected `nrow(covDf) > 0L` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-covariateData.R:328:3'): getDbOcmCovariateData produces valid CovariateData with Eunomia ──
Expected `nrow(refDf) > 0L` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-executeSpec-integration.R:475:3'): executeSpec works with drug_exposure domain ──
Expected `nrow(result) > 0` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 535 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [12s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(OdysseusCharacterizationModule)
>
> test_check("OdysseusCharacterizationModule")
attempting to download GiBleed
trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip'
Content type 'application/zip' length 6861852 bytes (6.5 MB)
==================================================
downloaded 6.5 MB
attempting to extract and load: /tmp/RtmpTxkfnw/working_dir/RtmpL0pwCT/GiBleed_5.3.zip to: /tmp/RtmpTxkfnw/working_dir/RtmpL0pwCT/GiBleed_5.3.sqlite
Saving _problems/test-covariateData-133.R
Connecting using SQLite driver
duckdb is storing downloaded extensions and secrets under ~/.duckdb:
i /data/localhost/ripley/.duckdb
This persists across sessions and is shared with the DuckDB CLI and other clients.
i Run duckdb(shared_home = FALSE) to use a temporary directory instead.
i See ?duckdb_storage for details and alternatives.
duckdb was built with libc++ (not libstdc++) on Linux, so DuckDB extensions are disabled:
* Loading a prebuilt (libstdc++) extension could crash R (https://github.com/duckdb/duckdb-r/issues/1107).
* INSTALL/LOAD of an extension will error, and automatic extension loading is off.
i Pass duckdb(allow_extensions = FALSE) to accept this and silence this message.
i Pass duckdb(allow_extensions = TRUE) to attempt loading anyway (may crash R).
i See ?duckdb for details.
duckdb was built with libc++ (not libstdc++) on Linux, so DuckDB extensions are disabled:
* Loading a prebuilt (libstdc++) extension could crash R (https://github.com/duckdb/duckdb-r/issues/1107).
* INSTALL/LOAD of an extension will error, and automatic extension loading is off.
i Pass duckdb(allow_extensions = FALSE) to accept this and silence this message.
i Pass duckdb(allow_extensions = TRUE) to attempt loading anyway (may crash R).
i See ?duckdb for details.
Connecting using SQLite driver
Cohorts created in table main.cohort
▶ == Executing 1 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
✓ Complete: 1 succeeded, 0 failed out of 1
duckdb is storing downloaded extensions and secrets under ~/.duckdb:
i /data/localhost/ripley/.duckdb
This persists across sessions and is shared with the DuckDB CLI and other clients.
i Run duckdb(shared_home = FALSE) to use a temporary directory instead.
i See ?duckdb_storage for details and alternatives.
duckdb was built with libc++ (not libstdc++) on Linux, so DuckDB extensions are disabled:
* Loading a prebuilt (libstdc++) extension could crash R (https://github.com/duckdb/duckdb-r/issues/1107).
* INSTALL/LOAD of an extension will error, and automatic extension loading is off.
i Pass duckdb(allow_extensions = FALSE) to accept this and silence this message.
i Pass duckdb(allow_extensions = TRUE) to attempt loading anyway (may crash R).
i See ?duckdb for details.
duckdb was built with libc++ (not libstdc++) on Linux, so DuckDB extensions are disabled:
* Loading a prebuilt (libstdc++) extension could crash R (https://github.com/duckdb/duckdb-r/issues/1107).
* INSTALL/LOAD of an extension will error, and automatic extension loading is off.
i Pass duckdb(allow_extensions = FALSE) to accept this and silence this message.
i Pass duckdb(allow_extensions = TRUE) to attempt loading anyway (may crash R).
i See ?duckdb for details.
Saving _problems/test-covariateData-323.R
Saving _problems/test-covariateData-328.R
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 2 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
• Executing spec 1002: Condition occurrence [-30, -1]
✓ 0 rows returned
✓ Complete: 2 succeeded, 0 failed out of 2
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 2 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
• Executing spec 9999: bad_spec
! Spec 9999 failed: Error executing SQL:
no such table: nonexistent_table_xyz
An error report has been created at /data/localhost/ripley/R/packages/tests-clang/OdysseusCharacterizationModule.Rcheck/tests/testthat/errorReportSql.txt
✓ Complete: 1 succeeded, 1 failed out of 2
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 1 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
✓ Complete: 1 succeeded, 0 failed out of 1
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 0 analysis spec(s) ============================
✓ Complete: 0 succeeded, 0 failed out of 0
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 1 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
✓ Complete: 1 succeeded, 0 failed out of 1
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Visit occurrence [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Procedure occurrence [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Measurement [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Drug exposure [-365, -1]
✓ 0 rows returned
Saving _problems/test-executeSpec-integration-475.R
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 3 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
• Executing spec 2001: Drug exposure [-365, -1]
✓ 0 rows returned
• Executing spec 3001: Procedure occurrence [-365, -1]
✓ 0 rows returned
✓ Complete: 3 succeeded, 0 failed out of 3
Cohorts created in table main.cohort
Connecting using SQLite driver
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
Executing SQL took 0.00874 secs
✓ Created #concept_sets_c with 1 concept set(s): gi
• Executing spec 10301: Concept set: gi (Condition occurrence) [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 100101: Cohort: Celecoxib [-365, -1]
✓ 0 rows returned
Characterization Analysis Plan
========================================
Analysis Windows: 1
Base Feature Domains: 1 of 9 enabled
condition_occurrence
Cohort Features: disabled
Concept Set Features: disabled
Single Node Analysis Specifications
========================================
Total specs: 1
base : 1
First 5 analyses:
[1] Condition occurrence [-30, -1] (id=1001)
Single Node Spec
------------------------------
Analysis ID: 1001
Name: Condition occurrence [-30, -1]
Table: condition_occurrence
Window: [-30, -1]
Type: start
Overlap: FALSE
ATC: FALSE
Concept Set: FALSE
Aggregated: TRUE
Source: base
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 535 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-covariateData.R:133:3'): .assembleCovariateData produces empty CovariateData when no results ──
Error: not an error
Backtrace:
▆
1. └─Eunomia::getEunomiaConnectionDetails() at test-covariateData.R:133:3
2. └─Eunomia::getDatabaseFile(...)
3. └─Eunomia::extractLoadData(...)
4. └─Eunomia::loadDataFiles(...)
5. ├─DBI::dbExecute(conn = connection, statement = statement)
6. └─DBI::dbExecute(conn = connection, statement = statement)
7. ├─DBI::dbSendStatement(conn, statement, ...)
8. └─DBI::dbSendStatement(conn, statement, ...)
9. ├─DBI::dbSendQuery(conn, statement, ...)
10. └─RSQLite::dbSendQuery(conn, statement, ...)
11. └─RSQLite (local) .local(conn, statement, ...)
12. ├─methods::new(...)
13. │ ├─methods::initialize(value, ...)
14. │ └─methods::initialize(value, ...)
15. └─RSQLite:::result_create(conn@ptr, statement)
── Failure ('test-covariateData.R:323:3'): getDbOcmCovariateData produces valid CovariateData with Eunomia ──
Expected `nrow(covDf) > 0L` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-covariateData.R:328:3'): getDbOcmCovariateData produces valid CovariateData with Eunomia ──
Expected `nrow(refDf) > 0L` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-executeSpec-integration.R:475:3'): executeSpec works with drug_exposure domain ──
Expected `nrow(result) > 0` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 535 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [22s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(OdysseusCharacterizationModule)
>
> test_check("OdysseusCharacterizationModule")
attempting to download GiBleed
trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip'
Content type 'application/zip' length 6861852 bytes (6.5 MB)
==================================================
downloaded 6.5 MB
attempting to extract and load: /tmp/RtmpYIIsfy/working_dir/RtmpfNQ42U/GiBleed_5.3.zip to: /tmp/RtmpYIIsfy/working_dir/RtmpfNQ42U/GiBleed_5.3.sqlite
Saving _problems/test-covariateData-133.R
Connecting using SQLite driver
duckdb is storing downloaded extensions and secrets under ~/.duckdb:
i /data/localhost/ripley/.duckdb
This persists across sessions and is shared with the DuckDB CLI and other clients.
i Run duckdb(shared_home = FALSE) to use a temporary directory instead.
i See ?duckdb_storage for details and alternatives.
Connecting using SQLite driver
Cohorts created in table main.cohort
▶ == Executing 1 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
✓ Complete: 1 succeeded, 0 failed out of 1
duckdb is storing downloaded extensions and secrets under ~/.duckdb:
i /data/localhost/ripley/.duckdb
This persists across sessions and is shared with the DuckDB CLI and other clients.
i Run duckdb(shared_home = FALSE) to use a temporary directory instead.
i See ?duckdb_storage for details and alternatives.
Saving _problems/test-covariateData-323.R
Saving _problems/test-covariateData-328.R
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 2 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
• Executing spec 1002: Condition occurrence [-30, -1]
✓ 0 rows returned
✓ Complete: 2 succeeded, 0 failed out of 2
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 2 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
• Executing spec 9999: bad_spec
! Spec 9999 failed: Error executing SQL:
no such table: nonexistent_table_xyz
An error report has been created at /data/localhost/ripley/R/packages/tests-devel/OdysseusCharacterizationModule.Rcheck/tests/testthat/errorReportSql.txt
✓ Complete: 1 succeeded, 1 failed out of 2
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 1 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
✓ Complete: 1 succeeded, 0 failed out of 1
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 0 analysis spec(s) ============================
✓ Complete: 0 succeeded, 0 failed out of 0
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 1 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
✓ Complete: 1 succeeded, 0 failed out of 1
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Visit occurrence [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Procedure occurrence [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Measurement [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 1001: Drug exposure [-365, -1]
✓ 0 rows returned
Saving _problems/test-executeSpec-integration-475.R
Cohorts created in table main.cohort
Connecting using SQLite driver
▶ == Executing 3 analysis spec(s) ============================
• Executing spec 1001: Condition occurrence [-365, -1]
✓ 0 rows returned
• Executing spec 2001: Drug exposure [-365, -1]
✓ 0 rows returned
• Executing spec 3001: Procedure occurrence [-365, -1]
✓ 0 rows returned
✓ Complete: 3 succeeded, 0 failed out of 3
Cohorts created in table main.cohort
Connecting using SQLite driver
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
Executing SQL took 0.00645 secs
✓ Created #concept_sets_c with 1 concept set(s): gi
• Executing spec 10301: Concept set: gi (Condition occurrence) [-365, -1]
✓ 0 rows returned
Cohorts created in table main.cohort
Connecting using SQLite driver
• Executing spec 100101: Cohort: Celecoxib [-365, -1]
✓ 0 rows returned
Characterization Analysis Plan
========================================
Analysis Windows: 1
Base Feature Domains: 1 of 9 enabled
condition_occurrence
Cohort Features: disabled
Concept Set Features: disabled
Single Node Analysis Specifications
========================================
Total specs: 1
base : 1
First 5 analyses:
[1] Condition occurrence [-30, -1] (id=1001)
Single Node Spec
------------------------------
Analysis ID: 1001
Name: Condition occurrence [-30, -1]
Table: condition_occurrence
Window: [-30, -1]
Type: start
Overlap: FALSE
ATC: FALSE
Concept Set: FALSE
Aggregated: TRUE
Source: base
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 535 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-covariateData.R:133:3'): .assembleCovariateData produces empty CovariateData when no results ──
Error: not an error
Backtrace:
▆
1. └─Eunomia::getEunomiaConnectionDetails() at test-covariateData.R:133:3
2. └─Eunomia::getDatabaseFile(...)
3. └─Eunomia::extractLoadData(...)
4. └─Eunomia::loadDataFiles(...)
5. ├─DBI::dbExecute(conn = connection, statement = statement)
6. └─DBI::dbExecute(conn = connection, statement = statement)
7. ├─DBI::dbSendStatement(conn, statement, ...)
8. └─DBI::dbSendStatement(conn, statement, ...)
9. ├─DBI::dbSendQuery(conn, statement, ...)
10. └─RSQLite::dbSendQuery(conn, statement, ...)
11. └─RSQLite (local) .local(conn, statement, ...)
12. ├─methods::new(...)
13. │ ├─methods::initialize(value, ...)
14. │ └─methods::initialize(value, ...)
15. └─RSQLite:::result_create(conn@ptr, statement)
── Failure ('test-covariateData.R:323:3'): getDbOcmCovariateData produces valid CovariateData with Eunomia ──
Expected `nrow(covDf) > 0L` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-covariateData.R:328:3'): getDbOcmCovariateData produces valid CovariateData with Eunomia ──
Expected `nrow(refDf) > 0L` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-executeSpec-integration.R:475:3'): executeSpec works with drug_exposure domain ──
Expected `nrow(result) > 0` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 535 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc