* using log directory ‘/data/localhost/ripley/R/packages/tests-clang-trunk/CodelistGenerator.Rcheck’ * using R Under development (unstable) (2026-09-03 r90476) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 23.1.0 flang version 23.1.0 * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-09-03 07:59:05 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 * 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/15s] 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 ... Running ‘testthat.R’ [28s/17s] [28s/17s] ERROR 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-tableOrphanCodes.R:3:3', '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-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 ── 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) ``(``) ── Error ('test-getCandidateCodes.R:7:5'): tests with mock db ────────────────── 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 ──────────────────────────── 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 ─────── 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 ─────────────────────── 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 ──────── 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 ── 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 ... [21s/35s] 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 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 See ‘/data/localhost/ripley/R/packages/tests-clang-trunk/CodelistGenerator.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:57.79, 91.17 + 9.73