Last updated on 2025-11-01 21:49:45 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| CodelistGenerator | 13 | ||
| CohortConstructor | 2 | 2 | 9 |
| IncidencePrevalence | 13 | ||
| OmopOnSpark | 1 | 12 | |
| PhenotypeR | 3 | 10 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 2, NOTE: 2, OK: 9
Version: 0.6.0
Check: tests
Result: ERROR
Running 'testthat.R' [11s]
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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CohortConstructor)
>
> test_check("CohortConstructor")
Starting 2 test processes
[ FAIL 2 | WARN 0 | SKIP 109 | PASS 0 ]
══ Skipped tests (109) ═════════════════════════════════════════════════════════
• On CRAN (109): 'test-addIndex.R:3:3', 'test-benchmark.R:2:3',
'test-collapseCohorts.R:2:3', 'test-collapseCohorts.R:99:3',
'test-collapseCohorts.R:173:3', 'test-collapseCohorts.R:260:3',
'test-copyCohorts.R:2:3', 'test-copyCohorts.R:52:3',
'test-copyCohorts.R:108:3', 'test-conceptCohort.R:2:3',
'test-conceptCohort.R:344:3', 'test-conceptCohort.R:547:3',
'test-conceptCohort.R:763:3', 'test-deathCohort.R:2:3',
'test-deathCohort.R:61:3', 'test-deathCohort.R:129:3',
'test-deathCohort.R:188:3', 'test-deathCohort.R:245:3',
'test-deathCohort.R:325:3', 'test-deathCohort.R:414:3',
'test-demographicsCohort.R:2:3', 'test-demographicsCohort.R:45:3',
'test-demographicsCohort.R:84:3', 'test-demographicsCohort.R:117:3',
'test-demographicsCohort.R:156:3', 'test-demographicsCohort.R:221:3',
'test-entryAtColumnDate.R:2:3', 'test-entryAtColumnDate.R:98:3',
'test-entryAtColumnDate.R:215:3', 'test-exitAtColumnDate.R:2:3',
'test-exitAtDate.R:2:3', 'test-exitAtDate.R:157:3',
'test-exitAtDate.R:246:3', 'test-matchCohorts.R:2:3',
'test-matchCohorts.R:71:3', 'test-matchCohorts.R:122:3',
'test-matchCohorts.R:183:3', 'test-matchCohorts.R:280:3',
'test-matchCohorts.R:316:3', 'test-intersectCohorts.R:2:3',
'test-intersectCohorts.R:51:3', 'test-intersectCohorts.R:102:3',
'test-intersectCohorts.R:149:3', 'test-intersectCohorts.R:206:3',
'test-intersectCohorts.R:287:3', 'test-intersectCohorts.R:338:3',
'test-intersectCohorts.R:394:3', 'test-intersectCohorts.R:486:3',
'test-intersectCohorts.R:606:3', 'test-intersectCohorts.R:669:3',
'test-intersectCohorts.R:723:3', 'test-measurementCohort.R:2:3',
'test-renameCohort.R:2:3', 'test-padCohortDate.R:2:3',
'test-padCohortDate.R:60:3', 'test-padCohortDate.R:141:3',
'test-padCohortDate.R:173:3', 'test-padCohortDate.R:327:3',
'test-padCohortDate.R:359:3', 'test-requireCohortIntersect.R:2:3',
'test-requireDateRange.R:2:3', 'test-requireDateRange.R:148:3',
'test-requireDateRange.R:253:3', 'test-requireConceptIntersect.R:2:3',
'test-requireConceptIntersect.R:153:3',
'test-requireConceptIntersect.R:267:3',
'test-requireConceptIntersect.R:377:3',
'test-requireConceptIntersect.R:455:3', 'test-requireDuration.R:2:3',
'test-requireDuration.R:104:3', 'test-requireIsEntry.R:2:3',
'test-requireIsEntry.R:57:3', 'test-requireIsEntry.R:128:3',
'test-requireIsEntry.R:145:3', 'test-requireIsEntry.R:216:3',
'test-requireIsEntry.R:359:3', 'test-requireMinCohortCount.R:2:3',
'test-requireMinCohortCount.R:122:3', 'test-requireTableIntersect.R:2:3',
'test-requireTableIntersect.R:150:3', 'test-requireTableIntersect.R:266:3',
'test-requireTableIntersect.R:383:3', 'test-sampleCohorts.R:2:3',
'test-sampleCohorts.R:35:3', 'test-sampleCohorts.R:64:3',
'test-sampleCohorts.R:89:3', 'test-sampleCohorts.R:109:3',
'test-sampleCohorts.R:130:3', 'test-stratifyCohorts.R:2:3',
'test-requireDemographics.R:2:3', 'test-requireDemographics.R:163:3',
'test-requireDemographics.R:210:3', 'test-requireDemographics.R:273:3',
'test-requireDemographics.R:298:3', 'test-requireDemographics.R:354:3',
'test-requireDemographics.R:384:3', 'test-requireDemographics.R:479:3',
'test-subsetCohorts.R:2:3', 'test-subsetCohorts.R:78:3',
'test-subsetCohorts.R:131:3', 'test-subsetCohorts.R:156:3',
'test-unionCohorts.R:2:3', 'test-unionCohorts.R:202:3',
'test-trimDemographics.R:2:3', 'test-trimDemographics.R:328:3',
'test-trimDemographics.R:449:3', 'test-yearCohorts.R:2:3',
'test-yearCohorts.R:139:3', 'test-yearCohorts.R:229:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-measurementCohort.R:395:3'): useRecordsBeforeObservation TRUE + edge cases ──
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortConstructor:::copyCdm(...) at test-measurementCohort.R:395:3
2. │ └─CDMConnector::dbSource(...) at D:\RCompile\CRANpkg\local\4.5\CohortConstructor.Rcheck\tests\testthat\setup.R:23:3
3. │ └─methods::is(con, "Pool")
4. └─base::loadNamespace(x)
5. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6. └─base (local) withOneRestart(expr, restarts[[1L]])
7. └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test-requireDemographics.R:455:3'): Missing sex/year of birth ───────
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortConstructor:::copyCdm(cdm_local) at test-requireDemographics.R:455:3
2. │ └─CDMConnector::dbSource(...) at D:\RCompile\CRANpkg\local\4.5\CohortConstructor.Rcheck\tests\testthat\setup.R:23:3
3. │ └─methods::is(con, "Pool")
4. └─base::loadNamespace(x) at D:\RCompile\CRANpkg\local\4.5\CohortConstructor.Rcheck\tests\testthat\setup.R:23:3
5. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6. └─base (local) withOneRestart(expr, restarts[[1L]])
7. └─base (local) doWithOneRestart(return(expr), restart)
[ FAIL 2 | WARN 0 | SKIP 109 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.6.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'a00_introduction.Rmd' using rmarkdown
--- finished re-building 'a00_introduction.Rmd'
--- re-building 'a01_building_base_cohorts.Rmd' using rmarkdown
Quitting from a01_building_base_cohorts.Rmd:24-34 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'duckdb'
---
Backtrace:
▆
1. └─base::library(duckdb)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a01_building_base_cohorts.Rmd' failed with diagnostics:
there is no package called 'duckdb'
--- failed re-building 'a01_building_base_cohorts.Rmd'
--- re-building 'a02_cohort_table_requirements.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 a02_cohort_table_requirements.Rmd:31-33 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a02_cohort_table_requirements.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building 'a02_cohort_table_requirements.Rmd'
--- re-building 'a03_require_demographics.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 a03_require_demographics.Rmd:28-30 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a03_require_demographics.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building 'a03_require_demographics.Rmd'
--- re-building 'a04_require_intersections.Rmd' using rmarkdown
--- finished re-building 'a04_require_intersections.Rmd'
--- re-building 'a05_update_cohort_start_end.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 a05_update_cohort_start_end.Rmd:37-48 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a05_update_cohort_start_end.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building 'a05_update_cohort_start_end.Rmd'
--- re-building 'a06_concatanate_cohorts.Rmd' using rmarkdown
--- finished re-building 'a06_concatanate_cohorts.Rmd'
--- re-building 'a07_filter_cohorts.Rmd' using rmarkdown
--- finished re-building 'a07_filter_cohorts.Rmd'
--- re-building 'a08_split_cohorts.Rmd' using rmarkdown
--- finished re-building 'a08_split_cohorts.Rmd'
--- re-building 'a09_combine_cohorts.Rmd' using rmarkdown
--- finished re-building 'a09_combine_cohorts.Rmd'
--- re-building 'a10_match_cohorts.Rmd' using rmarkdown
--- finished re-building 'a10_match_cohorts.Rmd'
--- re-building 'a11_benchmark.Rmd' using rmarkdown
--- finished re-building 'a11_benchmark.Rmd'
--- re-building 'a12_behind_the_scenes.Rmd' using rmarkdown
--- finished re-building 'a12_behind_the_scenes.Rmd'
SUMMARY: processing the following files failed:
'a01_building_base_cohorts.Rmd' 'a02_cohort_table_requirements.Rmd'
'a03_require_demographics.Rmd' 'a05_update_cohort_start_end.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.6.0
Check: installed package size
Result: NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
doc 5.1Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-windows-x86_64
Version: 0.6.0
Check: package dependencies
Result: ERROR
Packages required and available but unsuitable versions:
'omopgenerics', 'PatientProfiles'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 12
Version: 0.1.0
Check: package dependencies
Result: ERROR
Package required and available but unsuitable version: ‘omopgenerics’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64
Current CRAN status: NOTE: 3, OK: 10
Version: 0.2.0
Check: installed package size
Result: NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
doc 4.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64