* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/PhenotypeR.Rcheck’
* using R Under development (unstable) (2025-12-20 r89211)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* 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 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
* 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 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘PhenotypeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: addCodelistAttribute
> ### Title: Adds the cohort_codelist attribute to a cohort
> ### Aliases: addCodelistAttribute
> 
> ### ** Examples
> 
> ## No test: 
> library(PhenotypeR)
> 
> cdm <- mockPhenotypeR()
Error: 'buildAchillesTables' is not an exported object from 'namespace:CodelistGenerator'
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [17s/17s]
 [17s/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/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 ... [395s/243s] 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]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `summariseMeasurementUseInternal()`:
✖ `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$injuries)
 2.   └─MeasurementDiagnostics::summariseCohortMeasurementUse(...)
 3.     └─MeasurementDiagnostics:::summariseMeasurementUseInternal(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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 ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 3 ERRORs, 1 WARNING
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/PhenotypeR.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 5:17.57, 400.47 + 69.30