Last updated on 2024-12-01 14:49:13 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.4 | 5.99 | 708.01 | 714.00 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 3.09 | 554.60 | 557.69 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 1042.68 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 1101.67 | OK | |||
| r-devel-windows-x86_64 | 0.2.0 | 6.00 | 520.00 | 526.00 | OK | |
| r-patched-linux-x86_64 | 0.1.4 | 5.46 | 676.97 | 682.43 | ERROR | |
| r-release-linux-x86_64 | 0.1.3 | 4.20 | 666.46 | 670.66 | OK | |
| r-release-macos-arm64 | 0.2.0 | 198.00 | OK | |||
| r-release-macos-x86_64 | 0.2.0 | 336.00 | OK | |||
| r-release-windows-x86_64 | 0.2.0 | 6.00 | 497.00 | 503.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.0 | 253.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.2.0 | 379.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.2.0 | 6.00 | 553.00 | 559.00 | OK |
Version: 0.1.4
Check: dependencies in R code
Result: WARN
Missing or unexported objects:
‘visOmopResults::fxTable’ ‘visOmopResults::gtTable’
‘visOmopResults::splitNameLevel’
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64
Version: 0.1.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [282s/365s]
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(CohortSymmetry)
>
> test_check("CohortSymmetry")
Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
target signature 'duckdb_connection#Id'.
"duckdb_connection#ANY" would also be valid
===========================>--- 89% | ETA: 1s
`days_prior_observation` casted to character.
`group` is not present in settings.
===========================>--- 89% | ETA: 1s
===========================>--- 89% | ETA: 1s
===========================>--- 89% | ETA: 0s
===========================>--- 89% | ETA: 0s
`days_prior_observation` casted to character.
`days_prior_observation` casted to character.
-- 1 combination of 4 had index always before marker
`days_prior_observation` casted to character.
-- 1 combination of 4 had index always before marker
`days_prior_observation` casted to character.
Joining with `by = join_by(result_id, cdm_name)`
===========================>--- 89% | ETA: 0s
`days_prior_observation` casted to character.
Joining with `by = join_by(result_id, cdm_name)`
`days_prior_observation` casted to character.
`days_prior_observation` casted to character.
`days_prior_observation` casted to character.
[ FAIL 3 | WARN 73 | SKIP 53 | PASS 41 ]
══ Skipped tests (53) ══════════════════════════════════════════════════════════
• On CRAN (53): 'test-attrition.R:2:3', 'test-attrition.R:63:3',
'test-attrition.R:149:3', 'test-attrition.R:310:3', 'test-attrition.R:397:3',
'test-attrition.R:461:3', 'test-attrition.R:592:3', 'test-attrition.R:769:3',
'test-displayTable.R:30:3', 'test-displayTable.R:58:3',
'test-displayTable.R:86:3', 'test-eunomia.R:2:3', 'test-eunomia.R:65:3',
'test-generateSequenceCohortSet.R:3:3',
'test-generateSequenceCohortSet.R:20:3',
'test-generateSequenceCohortSet.R:96:3',
'test-generateSequenceCohortSet.R:153:3',
'test-generateSequenceCohortSet.R:205:3',
'test-generateSequenceCohortSet.R:259:3',
'test-generateSequenceCohortSet.R:288:3',
'test-generateSequenceCohortSet.R:330:3',
'test-generateSequenceCohortSet.R:356:3',
'test-generateSequenceCohortSet.R:427:3',
'test-generateSequenceCohortSet.R:515:3',
'test-generateSequenceCohortSet.R:663:3',
'test-generateSequenceCohortSet.R:751:3',
'test-generateSequenceCohortSet.R:764:3',
'test-generateSequenceCohortSet.R:776:3',
'test-generateSequenceCohortSet.R:788:3',
'test-generateSequenceCohortSet.R:800:3',
'test-generateSequenceCohortSet.R:818:3',
'test-generateSequenceCohortSet.R:836:3',
'test-generateSequenceCohortSet.R:848:3',
'test-generateSequenceCohortSet.R:859:3',
'test-generateSequenceCohortSet.R:870:3',
'test-generateSequenceCohortSet.R:894:3', 'test-plotSequenceRatio.R:41:3',
'test-plotSequenceRatio.R:85:3', 'test-plotTemporalSymmetry.R:42:3',
'test-plotTemporalSymmetry.R:86:3', 'test-summariseSequenceRatios.R:203:3',
'test-summariseSequenceRatios.R:415:3',
'test-summariseSequenceRatios.R:522:3',
'test-summariseSequenceRatios.R:604:3',
'test-summariseSequenceRatios.R:763:3',
'test-summariseSequenceRatios.R:801:3',
'test-summariseSequenceRatios.R:839:3',
'test-summariseSequenceRatios.R:877:3',
'test-summariseTemporalSymmetry.R:73:3',
'test-summariseTemporalSymmetry.R:98:3',
'test-summariseTemporalSymmetry.R:156:3', 'test-test-dbs.R:2:3',
'test-test-dbs.R:50:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-displayTable.R:14:3'): tableSequenceRatios - gt output ─────────
Error in `visOmopResults::formatEstimateName(visOmopResults::formatEstimateValue(result,
decimals = .options$decimals, decimalMark = .options$decimalMark,
bigMark = .options$bigMark), estimateNameFormat = estimateNameFormat,
keepNotFormatted = .options$keepNotFormatted, useFormatOrder = .options$useFormatOrder)`: unused argument (estimateNameFormat = estimateNameFormat)
Backtrace:
▆
1. └─CohortSymmetry::tableSequenceRatios(res) at test-displayTable.R:14:3
2. ├─dplyr::select(...)
3. ├─tidyr::pivot_wider(...)
4. ├─dplyr::mutate(...)
5. ├─dplyr::rename(...)
6. ├─... %>% ...
7. ├─dplyr::select(...)
8. ├─dplyr::mutate(...)
9. ├─dplyr::select(...)
10. └─visOmopResults::splitGroup(...)
11. └─omopgenerics:::splitNameLevelInternal(...)
12. └─omopgenerics::assertTable(...)
13. ├─omopgenerics:::checkDistinct(...)
14. ├─omopgenerics:::checkColumns2(...)
15. ├─omopgenerics:::checkNumberRows(...)
16. ├─omopgenerics:::checkNumberColumns(...)
17. ├─omopgenerics:::checkClass(...)
18. ├─omopgenerics:::checkNull(createCheckObject(x), null)
19. └─omopgenerics:::createCheckObject(x)
── Error ('test-plotTemporalSymmetry.R:25:3'): plot working ────────────────────
Error: 'splitNameLevel' is not an exported object from 'namespace:visOmopResults'
Backtrace:
▆
1. └─CohortSymmetry::plotTemporalSymmetry(result = result) at test-plotTemporalSymmetry.R:25:3
2. ├─dplyr::compute(...)
3. ├─dplyr::mutate(...)
4. ├─dplyr::mutate(...)
5. ├─dplyr::mutate(...)
6. ├─dplyr::filter(...)
7. ├─dplyr::rename(...)
8. ├─dplyr::ungroup(...)
9. ├─dplyr::select(...)
10. ├─tidyr::pivot_wider(...)
11. ├─tidyr::pivot_wider(...)
12. ├─dplyr::mutate(...)
13. ├─dplyr::group_by(...)
14. └─dplyr::select(...)
── Failure ('test-summariseTemporalSymmetry.R:30:3'): test summariseTemporalSymmetry ──
is.na(unique(temporal_symmetry$estimate_value)) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 3 | WARN 73 | SKIP 53 | PASS 41 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a01_Introduction.Rmd’ using rmarkdown
Quitting from lines 102-107 [unnamed-chunk-6] (a01_Introduction.Rmd)
Error: processing vignette 'a01_Introduction.Rmd' failed with diagnostics:
'splitNameLevel' is not an exported object from 'namespace:visOmopResults'
--- failed re-building ‘a01_Introduction.Rmd’
--- re-building ‘a02_Generate_a_sequence_cohort.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a02_Generate_a_sequence_cohort.Rmd’
--- re-building ‘a03_Summarise_sequence_ratios.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a03_Summarise_sequence_ratios.Rmd’
--- re-building ‘a04_Visualise_sequence_ratios.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 83-84 [unnamed-chunk-5] (a04_Visualise_sequence_ratios.Rmd)
Error: processing vignette 'a04_Visualise_sequence_ratios.Rmd' failed with diagnostics:
unused argument (estimateNameFormat = estimateNameFormat)
--- failed re-building ‘a04_Visualise_sequence_ratios.Rmd’
--- re-building ‘a05_Summarise_temporal_symmetry.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a05_Summarise_temporal_symmetry.Rmd’
--- re-building ‘a06_Visualise_temporal_symmetry.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 82-83 [unnamed-chunk-5] (a06_Visualise_temporal_symmetry.Rmd)
Error: processing vignette 'a06_Visualise_temporal_symmetry.Rmd' failed with diagnostics:
'splitNameLevel' is not an exported object from 'namespace:visOmopResults'
--- failed re-building ‘a06_Visualise_temporal_symmetry.Rmd’
SUMMARY: processing the following files failed:
‘a01_Introduction.Rmd’ ‘a04_Visualise_sequence_ratios.Rmd’
‘a06_Visualise_temporal_symmetry.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64
Version: 0.1.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [272s/389s]
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(CohortSymmetry)
>
> test_check("CohortSymmetry")
Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
target signature 'duckdb_connection#Id'.
"duckdb_connection#ANY" would also be valid
===========================>--- 89% | ETA: 0s
`days_prior_observation` casted to character.
`group` is not present in settings.
===========================>--- 89% | ETA: 0s
===========================>--- 89% | ETA: 1s
===========================>--- 89% | ETA: 0s
===========================>--- 89% | ETA: 0s
`days_prior_observation` casted to character.
===========================>--- 89% | ETA: 0s
`days_prior_observation` casted to character.
-- 1 combination of 4 had index always before marker
`days_prior_observation` casted to character.
-- 1 combination of 4 had index always before marker
`days_prior_observation` casted to character.
Joining with `by = join_by(result_id, cdm_name)`
===========================>--- 89% | ETA: 0s
`days_prior_observation` casted to character.
Joining with `by = join_by(result_id, cdm_name)`
===========================>--- 89% | ETA: 0s
`days_prior_observation` casted to character.
`days_prior_observation` casted to character.
`days_prior_observation` casted to character.
[ FAIL 3 | WARN 73 | SKIP 53 | PASS 41 ]
══ Skipped tests (53) ══════════════════════════════════════════════════════════
• On CRAN (53): 'test-attrition.R:2:3', 'test-attrition.R:63:3',
'test-attrition.R:149:3', 'test-attrition.R:310:3', 'test-attrition.R:397:3',
'test-attrition.R:461:3', 'test-attrition.R:592:3', 'test-attrition.R:769:3',
'test-displayTable.R:30:3', 'test-displayTable.R:58:3',
'test-displayTable.R:86:3', 'test-eunomia.R:2:3', 'test-eunomia.R:65:3',
'test-generateSequenceCohortSet.R:3:3',
'test-generateSequenceCohortSet.R:20:3',
'test-generateSequenceCohortSet.R:96:3',
'test-generateSequenceCohortSet.R:153:3',
'test-generateSequenceCohortSet.R:205:3',
'test-generateSequenceCohortSet.R:259:3',
'test-generateSequenceCohortSet.R:288:3',
'test-generateSequenceCohortSet.R:330:3',
'test-generateSequenceCohortSet.R:356:3',
'test-generateSequenceCohortSet.R:427:3',
'test-generateSequenceCohortSet.R:515:3',
'test-generateSequenceCohortSet.R:663:3',
'test-generateSequenceCohortSet.R:751:3',
'test-generateSequenceCohortSet.R:764:3',
'test-generateSequenceCohortSet.R:776:3',
'test-generateSequenceCohortSet.R:788:3',
'test-generateSequenceCohortSet.R:800:3',
'test-generateSequenceCohortSet.R:818:3',
'test-generateSequenceCohortSet.R:836:3',
'test-generateSequenceCohortSet.R:848:3',
'test-generateSequenceCohortSet.R:859:3',
'test-generateSequenceCohortSet.R:870:3',
'test-generateSequenceCohortSet.R:894:3', 'test-plotSequenceRatio.R:41:3',
'test-plotSequenceRatio.R:85:3', 'test-plotTemporalSymmetry.R:42:3',
'test-plotTemporalSymmetry.R:86:3', 'test-summariseSequenceRatios.R:203:3',
'test-summariseSequenceRatios.R:415:3',
'test-summariseSequenceRatios.R:522:3',
'test-summariseSequenceRatios.R:604:3',
'test-summariseSequenceRatios.R:763:3',
'test-summariseSequenceRatios.R:801:3',
'test-summariseSequenceRatios.R:839:3',
'test-summariseSequenceRatios.R:877:3',
'test-summariseTemporalSymmetry.R:73:3',
'test-summariseTemporalSymmetry.R:98:3',
'test-summariseTemporalSymmetry.R:156:3', 'test-test-dbs.R:2:3',
'test-test-dbs.R:50:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-displayTable.R:14:3'): tableSequenceRatios - gt output ─────────
Error in `visOmopResults::formatEstimateName(visOmopResults::formatEstimateValue(result,
decimals = .options$decimals, decimalMark = .options$decimalMark,
bigMark = .options$bigMark), estimateNameFormat = estimateNameFormat,
keepNotFormatted = .options$keepNotFormatted, useFormatOrder = .options$useFormatOrder)`: unused argument (estimateNameFormat = estimateNameFormat)
Backtrace:
▆
1. └─CohortSymmetry::tableSequenceRatios(res) at test-displayTable.R:14:3
2. ├─dplyr::select(...)
3. ├─tidyr::pivot_wider(...)
4. ├─dplyr::mutate(...)
5. ├─dplyr::rename(...)
6. ├─... %>% ...
7. ├─dplyr::select(...)
8. ├─dplyr::mutate(...)
9. ├─dplyr::select(...)
10. └─visOmopResults::splitGroup(...)
11. └─omopgenerics:::splitNameLevelInternal(...)
12. └─omopgenerics::assertTable(...)
13. ├─omopgenerics:::checkDistinct(...)
14. ├─omopgenerics:::checkColumns2(...)
15. ├─omopgenerics:::checkNumberRows(...)
16. ├─omopgenerics:::checkNumberColumns(...)
17. ├─omopgenerics:::checkClass(...)
18. ├─omopgenerics:::checkNull(createCheckObject(x), null)
19. └─omopgenerics:::createCheckObject(x)
── Error ('test-plotTemporalSymmetry.R:25:3'): plot working ────────────────────
Error: 'splitNameLevel' is not an exported object from 'namespace:visOmopResults'
Backtrace:
▆
1. └─CohortSymmetry::plotTemporalSymmetry(result = result) at test-plotTemporalSymmetry.R:25:3
2. ├─dplyr::compute(...)
3. ├─dplyr::mutate(...)
4. ├─dplyr::mutate(...)
5. ├─dplyr::mutate(...)
6. ├─dplyr::filter(...)
7. ├─dplyr::rename(...)
8. ├─dplyr::ungroup(...)
9. ├─dplyr::select(...)
10. ├─tidyr::pivot_wider(...)
11. ├─tidyr::pivot_wider(...)
12. ├─dplyr::mutate(...)
13. ├─dplyr::group_by(...)
14. └─dplyr::select(...)
── Failure ('test-summariseTemporalSymmetry.R:30:3'): test summariseTemporalSymmetry ──
is.na(unique(temporal_symmetry$estimate_value)) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 3 | WARN 73 | SKIP 53 | PASS 41 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64