• using R Under development (unstable) (2025-12-18 r89199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.7 (1)     Debian flang version 21.1.7 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘PhenotypeR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘PhenotypeR’ version ‘0.2.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• checking package namespace information ... OK
• checking package dependencies ... OK
• 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 ‘PhenotypeR’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [1s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
• checking loading without being on the library search path ... [1s/2s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... WARNING Missing or unexported object: ‘CodelistGenerator::buildAchillesTables’
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [8s/12s] OK
• checking Rd files ... [0s/1s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [1s/2s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [23s/29s] ERROR   Running ‘testthat.R’ [23s/29s] 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(PhenotypeR)   >   > test_check("PhenotypeR")   * Getting codelists from cohorts   * Getting index event breakdown   Getting counts of b codes for cohort cohort_1   * Getting diagnostics for measurement concepts   Saving _problems/test-codelistDiagnostics-90.R   [ FAIL 1 | WARN 4 | SKIP 21 | PASS 0 ]      ══ Skipped tests (21) ══════════════════════════════════════════════════════════   • On CRAN (17): 'test-addCodelistAttribute.R:2:3',     'test-addCodelistAttribute.R:70:3', 'test-addCodelistAttribute.R:118:3',     'test-codelistDiagnostics.R:2:3', 'test-codelistDiagnostics.R:48:3',     'test-cohortDiagnostics.R:2:3', 'test-cohortDiagnostics.R:51:3',     'test-databaseDiagnostics.R:2:3', 'test-dbms.R:3:3', 'test-dbms.R:25:3',     'test-getCohortExpectations.R:3:3', 'test-getCohortExpectations.R:26:3',     'test-getCohortExpectations.R:61:3', 'test-phenotypeDiagnostics.R:3:3',     'test-populationDiagnostics.R:2:3', 'test-shinyDiagnostics.R:3:3',     'test-shinyDiagnostics.R:53:3'   • empty test (4): 'test-cohortDiagnostics.R:144:1',     'test-cohortDiagnostics.R:148:1', 'test-cohortDiagnostics.R:152:1',     'test-cohortDiagnostics.R:158:1'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-codelistDiagnostics.R:90:3'): measurementDiagnostics working ───   Error in `summariseMeasurementUseInternal(cdm = cdm, codes = codes, cohort = cohort, timing = timing, timingName = timing, byConcept = byConcept, byYear = byYear, bySex = bySex, ageGroup = ageGroup, dateRange = dateRange, estimates = estimates, histogram = histogram, checks = checks)`: x `checks` a choice between: measurement_summary, measurement_value_as_number, and measurement_value_as_concept.   ! `checks` must be a choice between: measurement_summary, measurement_value_as_number, and measurement_value_as_concept; it can not contain NA; it can not be NULL.   Backtrace:       ▆    1. └─PhenotypeR::codelistDiagnostics(cdm$my_cohort) at test-codelistDiagnostics.R:90:3    2. └─MeasurementDiagnostics::summariseCohortMeasurementUse(...)    3. └─MeasurementDiagnostics:::summariseMeasurementUseInternal(...)    4. └─omopgenerics::assertChoice(checks, choices = allowedChecks)    5. └─omopgenerics:::errorMessage(...)    6. └─cli::cli_abort(message = message, call = call)    7. └─rlang::abort(...)      [ FAIL 1 | WARN 4 | SKIP 21 | PASS 0 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [386s/363s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘CodelistDiagnostics.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 CodelistDiagnostics.Rmd:60-62 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'CodelistDiagnostics.Rmd' failed with diagnostics: ✖ `checks` a choice between: measurement_summary,   measurement_value_as_number, and measurement_value_as_concept. ! `checks` must be a choice between: measurement_summary,   measurement_value_as_number, and measurement_value_as_concept; it can not   contain NA; it can not be NULL. --- failed re-building ‘CodelistDiagnostics.Rmd’ --- re-building ‘CohortDiagnostics.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘CohortDiagnostics.Rmd’ --- re-building ‘DatabaseDiagnostics.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: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘DatabaseDiagnostics.Rmd’ --- re-building ‘PhenotypeDiagnostics.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: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘PhenotypeDiagnostics.Rmd’ --- re-building ‘PhenotypeExpectations.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘PhenotypeExpectations.Rmd’ --- re-building ‘PopulationDiagnostics.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: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘PopulationDiagnostics.Rmd’ --- re-building ‘ShinyDiagnostics.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘ShinyDiagnostics.Rmd’ SUMMARY: processing the following file failed:   ‘CodelistDiagnostics.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs, 1 WARNING