• using R Under development (unstable) (2026-09-10 r90517)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 23.1.1     flang version 23.1.1
• running under: Fedora Linux 44 (Server Edition)
• using session charset: UTF-8 * current time: 2026-09-10 15:26:42 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘CodelistGenerator/DESCRIPTION’ ... OK
• this is package ‘CodelistGenerator’ version ‘4.1.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: 'duckdb'
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘CodelistGenerator’ can be installed ... OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [12s/13s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking R/sysdata.rda ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [29s/17s] ERROR   Running ‘testthat.R’ [28s/17s] 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 1 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-compareCodelists-108.R   Saving _problems/test-buildAchillesTables-55.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   Saving _problems/test-stratifyByRouteCategory-5.R   > test-stratifyByDoseUnit.R: Limiting to concept type, domains, and vocabularies of interest   > test-stratifyByDoseUnit.R: Getting concepts to include   > 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-classCodeSearch.R:3:3', 'test-codesFrom.R:2:3',     'test-codesFrom.R:118:3', 'test-compareCodelists.R:2:3',     'test-buildAchillesTables.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-summariseOrphanCodes.R:2:3',     'test-tableAchillesCodeUse.R:2:3', 'test-tableCodeUse.R:2:3',     'test-tableCodeUse.R:93:3', '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-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-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-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-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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [22s/35s] ERROR Error(s) in re-building vignettes: --- re-building ‘a01_GettingOmopCdmVocabularies.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘a01_GettingOmopCdmVocabularies.Rmd’ --- re-building ‘a02_ExploreCDMvocabulary.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘a02_ExploreCDMvocabulary.Rmd’ --- re-building ‘a03_TypesOfCodelist.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘a03_TypesOfCodelist.Rmd’ --- re-building ‘a04_GenerateCandidateCodelist.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- 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 [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘a05_GenerateVocabularyBasedCodelist.Rmd’ --- re-building ‘a06_ImportExport.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘a06_ImportExport.Rmd’ --- re-building ‘a08_ManipulateCodelists.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘a08_ManipulateCodelists.Rmd’ --- re-building ‘a09_RunCodelistDiagnostics.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- 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
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs