Running ‘testthat.R’ [598s/486s]
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 4 | WARN 47 | SKIP 48 | PASS 15 ]
  
  ══ Skipped tests (48) ══════════════════════════════════════════════════════════
  • On CRAN (48): 'test-deathDiagnostics.R:2:3', 'test-deathDiagnostics.R:116:3',
    'test-addCohortSurvival.R:71:3', 'test-addCohortSurvival.R:158:3',
    'test-addCohortSurvival.R:271:3', 'test-addCohortSurvival.R:377:3',
    'test-addCohortSurvival.R:489:3', 'test-addCohortSurvival.R:575:3',
    'test-addCohortSurvival.R:675:3', 'test-addCohortSurvival.R:762:3',
    'test-generateDeathCohort.R:2:3', 'test-generateDeathCohort.R:61:3',
    'test-generateDeathCohort.R:128:3', 'test-generateDeathCohort.R:194:3',
    'test-generateDeathCohort.R:261:3', 'test-generateDeathCohort.R:349:3',
    'test-generateDeathCohort.R:449:3', 'test-mockMGUS2cdm.R:2:3',
    'test-plotSurvival.R:2:3', 'test-plotSurvival.R:19:3',
    'test-plotSurvival.R:37:3', 'test-plotSurvival.R:57:3',
    'test-plotSurvival.R:77:3', 'test-plotSurvival.R:98:3',
    'test-plotSurvival.R:129:3', 'test-plotSurvival.R:149:3',
    'test-plotSurvival.R:172:3', 'test-plotSurvival.R:191:3',
    'test-tableSurvival.R:2:3', 'test-tableSurvival.R:88:3',
    'test-estimateSurvival.R:87:3', 'test-estimateSurvival.R:126:3',
    'test-estimateSurvival.R:176:3', 'test-estimateSurvival.R:343:3',
    'test-estimateSurvival.R:556:3', 'test-estimateSurvival.R:707:3',
    'test-estimateSurvival.R:1224:3', 'test-estimateSurvival.R:1350:3',
    'test-estimateSurvival.R:1372:3', 'test-estimateSurvival.R:1448:3',
    'test-estimateSurvival.R:1640:3', 'test-estimateSurvival.R:1763:3',
    'test-estimateSurvival.R:1793:3', 'test-estimateSurvival.R:1812:3',
    'test-estimateSurvival.R:1846:3', 'test-estimateSurvival.R:1979:3',
    'test-estimateSurvival.R:2106:3', 'test-estimateSurvival.R:2216:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-reexports-omopgenerics.R:17:3'): omopgenerics reexports work ──
  Expected `tableSurvival(surv_imported, type = "tibble")` to run without any errors.
  i Actually got a <simpleError> with text:
    'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
  ── Failure ('test-reexports-omopgenerics.R:30:3'): omopgenerics reexports work ──
  isTRUE(all.equal(surv, surv_nosup, check.attributes = FALSE)) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  ── Failure ('test-reexports-omopgenerics.R:34:3'): omopgenerics reexports work ──
  isTRUE(all.equal(surv, surv_nosup_imported, check.attributes = FALSE)) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Error ('test-estimateSurvival.R:9:3'): mgus example: no Competing risk ──────
  <vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
  Error in `dplyr::select(., c("cdm_name", "group_name", "group_level", "strata_name", 
      "strata_level", "variable_name", "variable_level", "estimate_name", 
      "estimate_type", "estimate_value", "additional_name", "additional_level", 
      "result_type", "outcome", "competing_outcome", "eventgap"))`: Can't select columns that don't exist.
  x Column `result_type` doesn't exist.
  Backtrace:
       ▆
    1. ├─... %>% asSurvivalResult() at test-estimateSurvival.R:9:3
    2. ├─CohortSurvival::asSurvivalResult(.)
    3. │ └─... %>% ...
    4. ├─dplyr::mutate(., estimate_value = as.numeric(.data$estimate_value))
    5. ├─visOmopResults::splitGroup(.)
    6. │ └─omopgenerics:::splitNameLevelInternal(...)
    7. │   └─omopgenerics::assertTable(...)
    8. │     ├─omopgenerics:::checkDistinct(...)
    9. │     ├─omopgenerics:::checkColumns2(...)
   10. │     ├─omopgenerics:::checkNumberRows(...)
   11. │     ├─omopgenerics:::checkNumberColumns(...)
   12. │     ├─omopgenerics:::checkClass(...)
   13. │     ├─omopgenerics:::checkNull(createCheckObject(x), null)
   14. │     └─omopgenerics:::createCheckObject(x)
   15. ├─visOmopResults::splitAdditional(.)
   16. │ └─omopgenerics:::splitNameLevelInternal(...)
   17. │   └─omopgenerics::assertTable(...)
   18. │     ├─omopgenerics:::checkDistinct(...)
   19. │     ├─omopgenerics:::checkColumns2(...)
   20. │     ├─omopgenerics:::checkNumberRows(...)
   21. │     ├─omopgenerics:::checkNumberColumns(...)
   22. │     ├─omopgenerics:::checkClass(...)
   23. │     ├─omopgenerics:::checkNull(createCheckObject(x), null)
   24. │     └─omopgenerics:::createCheckObject(x)
   25. ├─dplyr::select(...)
   26. ├─dplyr:::select.data.frame(...)
   27. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
   28. │   └─tidyselect:::eval_select_impl(...)
   29. │     ├─tidyselect:::with_subscript_errors(...)
   30. │     │ └─base::withCallingHandlers(...)
   31. │     └─tidyselect:::vars_select_eval(...)
   32. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   33. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   34. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   35. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   36. │               └─tidyselect:::eval_c(expr, data_mask, context_mask)
   37. │                 └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   38. │                   └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   39. │                     └─tidyselect:::as_indices_sel_impl(...)
   40. │                       └─tidyselect:::as_indices_impl(...)
   41. │                         └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
   42. │                           └─vctrs::vec_as_location(...)
   43. └─vctrs (local) `<fn>`()
   44.   └─vctrs:::stop_subscript_oob(...)
   45.     └─vctrs:::stop_subscript(...)
   46.       └─rlang::abort(...)
  
  [ FAIL 4 | WARN 47 | SKIP 48 | PASS 15 ]
  Error: Test failures
  Execution halted