Last updated on 2026-09-04 00:51:15 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 4.1.0 | 9.37 | 389.02 | 398.39 | OK | |
| r-devel-linux-x86_64-debian-gcc | 4.1.0 | 6.64 | 278.30 | 284.94 | OK | |
| r-devel-linux-x86_64-fedora-clang | 4.1.0 | 7.00 | 103.15 | 110.15 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 4.1.0 | 265.95 | OK | |||
| r-devel-windows-x86_64 | 4.1.0 | 12.00 | 321.00 | 333.00 | OK | |
| r-patched-linux-x86_64 | 4.1.0 | 10.14 | 373.34 | 383.48 | OK | |
| r-release-linux-x86_64 | 4.1.0 | 8.81 | 370.39 | 379.20 | OK | |
| r-release-macos-arm64 | 4.1.0 | 2.00 | 598.00 | 600.00 | OK | |
| r-release-macos-x86_64 | 4.1.0 | 6.00 | 587.00 | 593.00 | OK | |
| r-release-windows-x86_64 | 4.1.0 | 11.00 | 320.00 | 331.00 | OK | |
| r-oldrel-macos-arm64 | 4.1.0 | 2.00 | 1384.00 | 1386.00 | OK | |
| r-oldrel-macos-x86_64 | 4.1.0 | 6.00 | 1467.00 | 1473.00 | OK | |
| r-oldrel-windows-x86_64 | 4.1.0 | 14.00 | 405.00 | 419.00 | OK |
Version: 4.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [31s/38s]
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(CodelistGenerator)
Registered S3 method overwritten by 'CodelistGenerator':
method from
print.code_search omopgenerics
>
> test_check("CodelistGenerator")
Starting 2 test processes.
> test-asCodelist.R: Limiting to concept type, domains, and vocabularies of interest
> test-asCodelist.R: Getting concepts to include
> test-asCodelist.R: Adding descendants
> test-asCodelist.R: Search completed. Finishing up.
> test-asCodelist.R: v 4 candidate concepts identified
> test-asCodelist.R: Time taken: 0 minutes and 5 seconds
> test-asCodelist.R: ! No column specifying T/F for the different codes is detected
> test-asCodelist.R: ! No column specifying T/F for the different codes is detected
Saving _problems/test-buildAchillesTables-55.R
Saving _problems/test-compareCodelists-108.R
Saving _problems/test-getCandidateCodes-7.R
Saving _problems/test-mockVocabRef-2.R
> test-searchStrategy.R: Limiting to concept type, domains, and vocabularies of interest
> test-searchStrategy.R: Getting concepts to include
> test-searchStrategy.R: Adding descendants
> test-searchStrategy.R: Search completed. Finishing up.
> test-searchStrategy.R: v 5 candidate concepts identified
> test-searchStrategy.R: Time taken: 0 minutes and 0 seconds
> test-stratifyByDoseUnit.R: Limiting to concept type, domains, and vocabularies of interest
> test-stratifyByDoseUnit.R: Getting concepts to include
Saving _problems/test-stratifyByRouteCategory-5.R
> test-stratifyByDoseUnit.R: Adding descendants
> test-stratifyByDoseUnit.R: Search completed. Finishing up.
> test-stratifyByDoseUnit.R: v 2 candidate concepts identified
> test-stratifyByDoseUnit.R: Time taken: 0 minutes and 0 seconds
Saving _problems/test-subsetOnDomain-6.R
Saving _problems/test-subsetOnRouteCategory-6.R
Saving _problems/test-summariseAchillesCodeUse-66.R
> test-tidyWords.R: Symbols "-" will be ignored.
> test-tidyWords.R: `-` will be replaced by an empty space.
> test-tidyWords.R: Symbols "[", "¹", "⁸", "]", and "-" will be ignored.
> test-tidyWords.R: `-` will be replaced by an empty space.
[ FAIL 8 | WARN 0 | SKIP 53 | PASS 179 ]
══ Skipped tests (53) ══════════════════════════════════════════════════════════
• On CRAN (50): 'test-asCodelistWithDetails.R:2:3', 'test-availableATC.R:2:3',
'test-availableConceptClassIds.R:2:3', 'test-availableDomains.R:2:3',
'test-availableDoseForms.R:2:3', 'test-availableDoseUnit.R:2:3',
'test-availableDrugIngredients.R:2:3', 'test-availableRelationshipIds.R:2:3',
'test-availableRouteCategories.R:2:3', 'test-availableVocabularies.R:2:3',
'test-buildAchillesTables.R:2:3', 'test-classCodeSearch.R:3:3',
'test-codesFrom.R:2:3', 'test-codesFrom.R:118:3',
'test-compareCodelists.R:2:3', 'test-dbms.R:4:3', 'test-dbms.R:170:3',
'test-dbms.R:308:3', 'test-dbms.R:460:3', 'test-drugCodes.R:2:3',
'test-drugCodes.R:38:3', 'test-drugCodes.R:56:3', 'test-drugCodes.R:189:3',
'test-drugCodes.R:512:3', 'test-getCandidateCodes.R:441:3',
'test-getCandidateCodes.R:479:3', 'test-getMappings.R:2:3',
'test-intersectCodelists.R:2:3', 'test-intersectCodelists.R:48:3',
'test-stratifyByBrand.R:2:3', 'test-stratifyByConcept.R:2:3',
'test-subsetOnDoseUnit.R:2:3', 'test-subsetOnIngredientRange.R:2:3',
'test-subsetOnVocabulary.R:2:3', 'test-subsetToCodesInUse.R:2:3',
'test-summariseAchillesCodeUse.R:2:3', 'test-summariseCodeUse.R:2:3',
'test-summariseCodeUse.R:361:3', 'test-summariseCodeUse.R:604:3',
'test-summariseCodeUse.R:911:3', 'test-summariseCodeUse.R:937:3',
'test-summariseCodeUse.R:969:3', 'test-summariseOrphanCodes.R:2:3',
'test-tableAchillesCodeUse.R:2:3', 'test-tableCodeUse.R:2:3',
'test-tableCodeUse.R:93:3', 'test-tableOrphanCodes.R:3:3',
'test-unionCodelists.R:2:3', 'test-unionCodelists.R:47:3',
'test-vocabUtilities.R:2:3'
• Skipping (1): 'test-summariseCodeUse.R:654:3'
• Sys.getenv("CDM5_SQL_SERVER_SERVER") == "" is TRUE (1):
'test-subsetToCodesInUse.R:57:3'
• Sys.getenv("darwinDbDatabaseServer") == "" is TRUE (1):
'test-synthea_sql_server.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-buildAchillesTables.R:55:3'): test buildAchillesTables when not all tables required are present ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb()) at test-buildAchillesTables.R:55:3
2. ├─base::loadNamespace(x)
3. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
4. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
5. │ │ └─base (local) doWithOneRestart(return(expr), restart)
6. │ └─base::stop(cond)
7. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-compareCodelists.R:108:5'): comparing two codelists- same codes found different ways ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockVocabRef(backends[[i]])`: The package "duckdb" is required.
Backtrace:
▆
1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-compareCodelists.R:108:5
2. └─rlang::check_installed("duckdb")
── Error ('test-getCandidateCodes.R:7:5'): tests with mock db ──────────────────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockVocabRef(backends[[i]])`: The package "duckdb" is required.
Backtrace:
▆
1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-getCandidateCodes.R:7:5
2. └─rlang::check_installed("duckdb")
── Error ('test-mockVocabRef.R:2:3'): mock vocab db ────────────────────────────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockVocabRef("database")`: The package "duckdb" is required.
Backtrace:
▆
1. └─CodelistGenerator::mockVocabRef("database") at test-mockVocabRef.R:2:3
2. └─rlang::check_installed("duckdb")
── Error ('test-stratifyByRouteCategory.R:5:5'): stratify by route works ───────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockVocabRef(backends[[i]])`: The package "duckdb" is required.
Backtrace:
▆
1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-stratifyByRouteCategory.R:5:5
2. └─rlang::check_installed("duckdb")
── Error ('test-subsetOnDomain.R:6:5'): subset on domain ───────────────────────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockVocabRef(backends[[i]])`: The package "duckdb" is required.
Backtrace:
▆
1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-subsetOnDomain.R:6:5
2. └─rlang::check_installed("duckdb")
── Error ('test-subsetOnRouteCategory.R:6:5'): subset on route category ────────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockVocabRef(backends[[i]])`: The package "duckdb" is required.
Backtrace:
▆
1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-subsetOnRouteCategory.R:6:5
2. └─rlang::check_installed("duckdb")
── Error ('test-summariseAchillesCodeUse.R:66:3'): achilles code use: multipe codelists ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockVocabRef("database")`: The package "duckdb" is required.
Backtrace:
▆
1. └─CodelistGenerator::mockVocabRef("database") at test-summariseAchillesCodeUse.R:66:3
2. └─rlang::check_installed("duckdb")
[ FAIL 8 | WARN 0 | SKIP 53 | PASS 179 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 4.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘a01_GettingOmopCdmVocabularies.Rmd’ using rmarkdown
--- finished re-building ‘a01_GettingOmopCdmVocabularies.Rmd’
--- re-building ‘a02_ExploreCDMvocabulary.Rmd’ using rmarkdown
--- finished re-building ‘a02_ExploreCDMvocabulary.Rmd’
--- re-building ‘a03_TypesOfCodelist.Rmd’ using rmarkdown
--- finished re-building ‘a03_TypesOfCodelist.Rmd’
--- re-building ‘a04_GenerateCandidateCodelist.Rmd’ using rmarkdown
--- finished re-building ‘a04_GenerateCandidateCodelist.Rmd’
--- re-building ‘a05_GenerateVocabularyBasedCodelist.Rmd’ using rmarkdown
trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip'
Content type 'application/zip' length 593048982 bytes (565.6 MB)
==================================================
downloaded 565.6 MB
--- finished re-building ‘a05_GenerateVocabularyBasedCodelist.Rmd’
--- re-building ‘a06_ImportExport.Rmd’ using rmarkdown
--- finished re-building ‘a06_ImportExport.Rmd’
--- re-building ‘a08_ManipulateCodelists.Rmd’ using rmarkdown
--- finished re-building ‘a08_ManipulateCodelists.Rmd’
--- re-building ‘a09_RunCodelistDiagnostics.Rmd’ using rmarkdown
--- finished re-building ‘a09_RunCodelistDiagnostics.Rmd’
--- re-building ‘a10_CodelistGeneratorBenchmark.Rmd’ using rmarkdown
trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip'
Content type 'application/zip' length 593048982 bytes (565.6 MB)
==================================================
downloaded 565.6 MB
Quitting from a10_CodelistGeneratorBenchmark.Rmd:25-47 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'duckdb'
---
Backtrace:
▆
1. └─base::library(duckdb)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a10_CodelistGeneratorBenchmark.Rmd' failed with diagnostics:
there is no package called 'duckdb'
--- failed re-building ‘a10_CodelistGeneratorBenchmark.Rmd’
SUMMARY: processing the following file failed:
‘a10_CodelistGeneratorBenchmark.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang