Package: PhenotypeR
Check: dependencies in R code
New result: WARNING
  Missing or unexported object: ‘CodelistGenerator::buildAchillesTables’

Package: PhenotypeR
Check: re-building of vignette outputs
New result: 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

Package: PhenotypeR
Check: tests
New result: ERROR
    Running ‘testthat.R’ [12s/12s]
  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