Running ‘testthat.R’ [16s/19s]
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(CohortSurvival)
  > 
  > test_check("CohortSurvival")
  Starting 2 test processes
  [ FAIL 2 | WARN 0 | SKIP 42 | PASS 0 ]
  
  ══ Skipped tests (42) ══════════════════════════════════════════════════════════
  • On CRAN (42): 'test-benchmarkCohortSurvival.R:2:3',
    'test-benchmarkCohortSurvival.R:61:3', 'test-addCohortSurvival.R:43:3',
    'test-addCohortSurvival.R:149:3', 'test-addCohortSurvival.R:235:3',
    'test-addCohortSurvival.R:314:3', 'test-addCohortSurvival.R:399:3',
    'test-addCohortSurvival.R:479:3', 'test-addCohortSurvival.R:491:3',
    'test-addCohortSurvival.R:564:3', 'test-addCohortSurvival.R:623:3',
    'test-generateDeathCohort.R:2:3', 'test-generateDeathCohort.R:29:3',
    'test-generateDeathCohort.R:61:3', 'test-generateDeathCohort.R:104:3',
    'test-generateDeathCohort.R:132:3', 'test-generateDeathCohort.R:184:3',
    'test-generateDeathCohort.R:223:3', 'test-mockMGUS2cdm.R:2:3',
    'test-plotSurvival.R:2:3', 'test-plotSurvival.R:20:3',
    'test-plotSurvival.R:38:3', 'test-plotSurvival.R:58:3',
    'test-plotSurvival.R:78:3', 'test-plotSurvival.R:99:3',
    'test-plotSurvival.R:117:3', 'test-plotSurvival.R:137:3',
    'test-survivalSummary.R:2:3', 'test-estimateSurvival.R:104:3',
    'test-estimateSurvival.R:148:3', 'test-estimateSurvival.R:202:3',
    'test-estimateSurvival.R:345:3', 'test-estimateSurvival.R:531:3',
    'test-estimateSurvival.R:913:3', 'test-estimateSurvival.R:1010:3',
    'test-estimateSurvival.R:1028:3', 'test-estimateSurvival.R:1061:3',
    'test-estimateSurvival.R:1110:3', 'test-estimateSurvival.R:1277:3',
    'test-estimateSurvival.R:1375:3', 'test-estimateSurvival.R:1403:3',
    'test-estimateSurvival.R:1422:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-addCohortSurvival.R:22:3'): working example ────────────────────
  Error in `newOmopTable(cdm[[nm]])`: race_concept_id and ethnicity_concept_id are not present in table person
  Backtrace:
      ▆
   1. └─PatientProfiles::mockPatientProfiles(cohort1 = cohort, observation_period = observation_period) at test-addCohortSurvival.R:22:3
   2.   └─CDMConnector::cdm_from_con(...)
   3.     └─omopgenerics::newCdmReference(...)
   4.       └─omopgenerics:::validateCdmReference(cdm)
   5.         └─omopgenerics::newOmopTable(cdm[[nm]])
   6.           └─omopgenerics:::checkColumnsCdm(table, name, cols)
   7.             └─cli::cli_abort(...)
   8.               └─rlang::abort(...)
  ── Error ('test-estimateSurvival.R:8:3'): mgus example: no Competing risk ──────
  Error in `newOmopTable(cdm[[nm]])`: race_concept_id and ethnicity_concept_id are not present in table person
  Backtrace:
      ▆
   1. └─CohortSurvival::mockMGUS2cdm() at test-estimateSurvival.R:8:3
   2.   └─CDMConnector::cdm_from_con(...)
   3.     └─omopgenerics::newCdmReference(...)
   4.       └─omopgenerics:::validateCdmReference(cdm)
   5.         └─omopgenerics::newOmopTable(cdm[[nm]])
   6.           └─omopgenerics:::checkColumnsCdm(table, name, cols)
   7.             └─cli::cli_abort(...)
   8.               └─rlang::abort(...)
  
  [ FAIL 2 | WARN 0 | SKIP 42 | PASS 0 ]
  Error: Test failures
  Execution halted