Package: bayesCureRateModel
Check: for code/documentation mismatches
New result: WARNING
  Codoc mismatches from Rd file 'Surv.Rd':
  Surv
    Code: function(time, time2, event, type = c("right", "left",
                   "interval", "counting", "interval2"), origin = 0)
    Docs: function(time, time2, event, type = c("right", "left",
                   "interval", "counting", "interval2", "mstate"), origin
                   = 0)
    Mismatches in argument default values:
      Name: 'type' Code: c("right", "left", "interval", "counting", "interval2") Docs: c("right", "left", "interval", "counting", "interval2", "mstate")

Package: CohortSurvival
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘a01_Single_event_of_interest.Rmd’ using rmarkdown
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘a01_Single_event_of_interest.Rmd’
  
  --- re-building ‘a02_Competing_risk_survival.Rmd’ using rmarkdown
  
  Quitting from a02_Competing_risk_survival.Rmd:86-94 [unnamed-chunk-8]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/purrr_error_indexed>
  Error in `purrr::pmap()`:
  ℹ In index: 1.
  Caused by error in `dplyr::mutate()`:
  ℹ In argument: `strata_level = .data$strata`.
  ---
  Backtrace:
       ▆
    1. ├─CohortSurvival::estimateCompetingRiskSurvival(...)
    2. │ └─purrr::pmap(...)
    3. │   └─purrr:::pmap_("list", .l, .f, ..., .progress = .progress)
    4. │     ├─purrr:::with_indexed_errors(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     ├─purrr:::call_with_cleanup(...)
    7. │     └─CohortSurvival (local) .f(...)
    8. │       └─CohortSurvival:::estimateSurvival(...)
    9. │         └─CohortSurvival:::competingRiskSurvival(...)
   10. │           ├─dplyr::mutate(...)
   11. │           └─dplyr:::mutate.data.frame(...)
   12. │             └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
   13. │               ├─base::withCallingHandlers(...)
   14. │               └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
   15. │                 └─mask$eval_all_mutate(quo)
   16. │                   └─dplyr (local) eval()
   17. ├─strata
   18. ├─rlang:::`$.rlang_data_pronoun`(.data, strata)
   19. │ └─rlang:::data_pronoun_get(...)
   20. ├─rlang:::abort_data_pronoun(x, call = y)
   21. │ └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call)
   22. │   └─rlang:::signal_abort(cnd, .file)
   23. │     └─base::signalCondition(cnd)
   24. └─dplyr (local) `<fn>`(`<rln_____>`)
  Caused by error in `.data$strata`:
  ! Column `strata` not found in `.data`.
  ---
  Backtrace:
       ▆
    1. ├─CohortSurvival::estimateCompetingRiskSurvival(...)
    2. │ └─purrr::pmap(...)
    3. │   └─purrr:::pmap_("list", .l, .f, ..., .progress = .progress)
    4. │     ├─purrr:::with_indexed_errors(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     ├─purrr:::call_with_cleanup(...)
    7. │     └─CohortSurvival (local) .f(...)
    8. │       └─CohortSurvival:::estimateSurvival(...)
    9. │         └─CohortSurvival:::competingRiskSurvival(...)
   10. │           ├─dplyr::mutate(...)
   11. │           └─dplyr:::mutate.data.frame(...)
   12. │             └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
   13. │               ├─base::withCallingHandlers(...)
   14. │               └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
   15. │                 └─mask$eval_all_mutate(quo)
   16. │                   └─dplyr (local) eval()
   17. ├─strata
   18. ├─rlang:::`$.rlang_data_pronoun`(.data, strata)
   19. │ └─rlang:::data_pronoun_get(...)
   20. └─rlang:::abort_data_pronoun(x, call = y)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'a02_Competing_risk_survival.Rmd' failed with diagnostics:
  ℹ In index: 1.
  Caused by error in `dplyr::mutate()`:
  ℹ In argument: `strata_level = .data$strata`.
  Caused by error in `.data$strata`:
  ! Column `strata` not found in `.data`.
  --- failed re-building ‘a02_Competing_risk_survival.Rmd’
  
  --- re-building ‘a03_Further_survival_analyses.Rmd’ using rmarkdown
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘a03_Further_survival_analyses.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘a02_Competing_risk_survival.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: CohortSurvival
Check: tests
New result: ERROR
    Running ‘testthat.R’ [606s/462s]
  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.
    > test-addCohortSurvival.R: ===============>---------------   50% | ETA:  2s
    > test-estimateSurvival.R: ==================>------------   60% | ETA:  3s
    > test-estimateSurvival.R: ========================>------   80% | ETA:  2s
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-plotSurvival.R: ==================>------------   60% | ETA:  3s
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
    > test-plotSurvival.R: ========================>------   80% | ETA:  2s
    > test-plotSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-plotSurvival.R: Getting overall estimates
    > test-plotSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-plotSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-plotSurvival.R: Getting overall estimates
    > test-plotSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-plotSurvival.R: ============>------------------   40% | ETA:  3s
    > test-estimateSurvival.R: ==================>------------   60% | ETA:  3s
    > test-estimateSurvival.R: ========================>------   80% | ETA:  2s
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-plotSurvival.R: ==================>------------   60% | ETA:  6s
    > test-plotSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_test_empty'
    > test-plotSurvival.R: Getting overall estimates
    > test-plotSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-plotSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
    > test-plotSurvival.R: Getting overall estimates
    > test-plotSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression_fake_empty' and competing outcome cohort 'dea
    > test-estimateSurvival.R: th_cohort'
    > test-reexports-omopgenerics.R: ============>------------------   40% | ETA:  3s
    > test-reexports-omopgenerics.R: ==================>------------   60% | ETA:  6s
    > test-reexports-omopgenerics.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-estimateSurvival.R: 
    > test-estimateSurvival.R: -- No results for competing risk analysis --------------------------------------
    > test-estimateSurvival.R: Competing risk variable must have three levels.Do you have at least 1
    > test-estimateSurvival.R: individual for:
    > test-estimateSurvival.R: * 1) censored without event,
    > test-estimateSurvival.R: * 2) censored at outcome event of intest, and
    > test-estimateSurvival.R: * 3) censored at outcome competing event?
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_test_emp
    > test-estimateSurvival.R: ty'
    > test-reexports-omopgenerics.R: Getting overall estimates
    > test-reexports-omopgenerics.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-reexports-omopgenerics.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
    > test-estimateSurvival.R: 
    > test-estimateSurvival.R: -- No results for competing risk analysis --------------------------------------
    > test-estimateSurvival.R: Competing risk variable must have three levels.Do you have at least 1
    > test-estimateSurvival.R: individual for:
    > test-estimateSurvival.R: * 1) censored without event,
    > test-estimateSurvival.R: * 2) censored at outcome event of intest, and
    > test-estimateSurvival.R: * 3) censored at outcome competing event?
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression_fake_empty' and competing outcome cohort 'dea
    > test-estimateSurvival.R: th_test_empty'
    > test-reexports-omopgenerics.R: Getting overall estimates
    Saving _problems/test-reexports-omopgenerics-57.R
    > test-estimateSurvival.R: 
    > test-estimateSurvival.R: -- No results for competing risk analysis --------------------------------------
    > test-estimateSurvival.R: Competing risk variable must have three levels.Do you have at least 1
    > test-estimateSurvival.R: individual for:
    > test-estimateSurvival.R: * 1) censored without event,
    > test-estimateSurvival.R: * 2) censored at outcome event of intest, and
    > test-estimateSurvival.R: * 3) censored at outcome competing event?
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: ============>------------------   40% | ETA:  3s
    > test-estimateSurvival.R: ========================>------   80% | ETA:  2s
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'progression'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: ==================>------------   60% | ETA:  2s
    > test-estimateSurvival.R: ========================>------   80% | ETA:  2s
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: ========================>------   80% | ETA:  1s
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: ==================>------------   60% | ETA:  3s
    > test-estimateSurvival.R: ========================>------   80% | ETA:  2s
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: `eventgap` eliminated from settings as all elements are NA.
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: `eventgap` eliminated from settings as all elements are NA.
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis_2020' and outcome cohort 'death_cohort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis_2020', outcome cohort 'progression' and competing outcome cohort 'death_coh
    > test-estimateSurvival.R: ort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: ==================>------------   60% | ETA:  3s
    > test-estimateSurvival.R: ========================>------   80% | ETA:  2s
    > test-estimateSurvival.R: ============>------------------   40% | ETA:  3s
    > test-estimateSurvival.R: ========================>------   80% | ETA:  2s
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: ==================>------------   60% | ETA:  3s
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    > test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
    > test-estimateSurvival.R: Getting overall estimates
    > test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
    [ FAIL 1 | WARN 10 | SKIP 56 | PASS 66 ]
    
    ══ Skipped tests (56) ══════════════════════════════════════════════════════════
    • On CRAN (56): 'test-asSurvivalResult.R:2:3', 'test-asSurvivalResult.R:19:3',
      'test-asSurvivalResult.R:54:3', 'test-asSurvivalResult.R:94:3',
      'test-asSurvivalResult.R:148:3', 'test-asSurvivalResult.R:203:3',
      'test-asSurvivalResult.R:246:3', 'test-asSurvivalResult.R:289:3',
      'test-asSurvivalResult.R:330:3', 'test-addCohortSurvival.R:2:3',
      'test-addCohortSurvival.R:73:3', 'test-addCohortSurvival.R:160:3',
      'test-addCohortSurvival.R:259:3', 'test-addCohortSurvival.R:351:3',
      'test-addCohortSurvival.R:455:3', 'test-addCohortSurvival.R:541:3',
      'test-addCohortSurvival.R:633:3', 'test-addCohortSurvival.R:712:3',
      'test-mockMGUS2cdm.R:2:3', 'test-plotSurvival.R:2:3',
      'test-plotSurvival.R:19:3', 'test-plotSurvival.R:52:3',
      'test-plotSurvival.R:83:3', 'test-plotSurvival.R:126:3',
      'test-plotSurvival.R:134:3', 'test-plotSurvival.R:157:3',
      'test-plotSurvival.R:186:3', 'test-reexports-omopgenerics.R:3:3',
      'test-riskTable.R:2:3', 'test-riskTable.R:65:3', 'test-tableSurvival.R:2:3',
      'test-tableSurvival.R:91:3', 'test-tableSurvival.R:117:3',
      'test-tableSurvival.R:141:3', 'test-tableSurvival.R:151:3',
      'test-tableSurvivalAttrition.R:2:3', 'test-estimateSurvival.R:80:3',
      'test-estimateSurvival.R:131:3', 'test-estimateSurvival.R:193:3',
      'test-estimateSurvival.R:351:3', 'test-estimateSurvival.R:556:3',
      'test-estimateSurvival.R:698:3', 'test-estimateSurvival.R:1166:3',
      'test-estimateSurvival.R:1278:3', 'test-estimateSurvival.R:1300:3',
      'test-estimateSurvival.R:1367:3', 'test-estimateSurvival.R:1552:3',
      'test-estimateSurvival.R:1665:3', 'test-estimateSurvival.R:1695:3',
      'test-estimateSurvival.R:1714:3', 'test-estimateSurvival.R:1747:3',
      'test-estimateSurvival.R:1876:3', 'test-estimateSurvival.R:2090:3',
      'test-estimateSurvival.R:2222:5', 'test-estimateSurvival.R:2435:3',
      'test-estimateSurvival.R:2467:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-reexports-omopgenerics.R:53:3'): omopgenerics filterSettings ───
    <purrr_error_indexed/rlang_error/error/condition>
    Error in `purrr::pmap(expand.grid(target_idx = seq_along(targetCohortId), outcome_idx = seq_along(outcomeCohortId), competing_outcome_idx = seq_along(competingOutcomeCohortId)), function(target_idx, outcome_idx, competing_outcome_idx) {     working_target_id <- targetCohortId[target_idx]     working_target <- dplyr::pull(dplyr::filter(omopgenerics::settings(cdm[[targetCohortTable]]), .data$cohort_definition_id == working_target_id), "cohort_name")     working_outcome_id <- outcomeCohortId[outcome_idx]     working_outcome <- dplyr::pull(dplyr::filter(omopgenerics::settings(cdm[[outcomeCohortTable]]), .data$cohort_definition_id == working_outcome_id), "cohort_name")     working_competing_outcome_id <- competingOutcomeCohortId[competing_outcome_idx]     working_competing_outcome <- dplyr::pull(dplyr::filter(omopgenerics::settings(cdm[[competingOutcomeCohortTable]]), .data$cohort_definition_id == working_competing_outcome_id), "cohort_name")     cli::cli_inform("- Getting survival for target cohort '{working_target}', outcome cohort '{working_outcome}' and\n                      competing outcome cohort '{working_competing_outcome}'")     surv <- estimateSurvival(cdm = cdm, targetCohortTable = targetCohortTable, targetCohortId = working_target_id, outcomeCohortTable = outcomeCohortTable, outcomeCohortId = working_outcome_id, outcomeDateVariable = outcomeDateVariable, outcomeWashout = outcomeWashout, competingOutcomeCohortTable = competingOutcomeCohortTable, competingOutcomeCohortId = working_competing_outcome_id, competingOutcomeDateVariable = competingOutcomeDateVariable, competingOutcomeWashout = competingOutcomeWashout, censorOnCohortExit = censorOnCohortExit,          censorOnDate = censorOnDate, followUpDays = followUpDays, strata = strata, eventGap = eventGap, estimateGap = estimateGap, restrictedMeanFollowUp = restrictedMeanFollowUp, minimumSurvivalDays = minimumSurvivalDays)     if (!is.null(attr(surv, "cohort_attrition"))) {         attrition <- dplyr::filter(dplyr::collect(dplyr::mutate(attr(surv, "cohort_attrition"), target_cohort = working_target, outcome = working_outcome, competing_outcome = working_competing_outcome)), .data$cohort_definition_id == working_target_id)     }     else {         attrition <- attr(surv, "cohort_attrition")     }     events <- attr(surv, "events")     summary <- attr(surv, "summary")     return(list(surv = surv, attrition = attrition, events = events, summary = summary)) })`: i In index: 1.
    Caused by error in `dplyr::mutate()`:
    i In argument: `strata_level = .data$strata`.
    Caused by error in `.data$strata`:
    ! Column `strata` not found in `.data`.
    Backtrace:
         ▆
      1. ├─CohortSurvival::estimateCompetingRiskSurvival(...) at test-reexports-omopgenerics.R:53:3
      2. │ └─purrr::pmap(...)
      3. │   └─purrr:::pmap_("list", .l, .f, ..., .progress = .progress)
      4. │     ├─purrr:::with_indexed_errors(...)
      5. │     │ └─base::withCallingHandlers(...)
      6. │     ├─purrr:::call_with_cleanup(...)
      7. │     └─CohortSurvival (local) .f(...)
      8. │       └─CohortSurvival:::estimateSurvival(...)
      9. │         └─CohortSurvival:::competingRiskSurvival(...)
     10. │           ├─dplyr::mutate(...)
     11. │           └─dplyr:::mutate.data.frame(...)
     12. │             └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
     13. │               ├─base::withCallingHandlers(...)
     14. │               └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
     15. │                 └─mask$eval_all_mutate(quo)
     16. │                   └─dplyr (local) eval()
     17. ├─strata
     18. ├─rlang:::`$.rlang_data_pronoun`(.data, strata)
     19. │ └─rlang:::data_pronoun_get(...)
     20. ├─rlang:::abort_data_pronoun(x, call = y)
     21. │ └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call)
     22. │   └─rlang:::signal_abort(cnd, .file)
     23. │     └─base::signalCondition(cnd)
     24. ├─dplyr (local) `<fn>`(`<rln_____>`)
     25. │ └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
     26. │   └─rlang:::signal_abort(cnd, .file)
     27. │     └─base::signalCondition(cnd)
     28. └─purrr (local) `<fn>`(`<dply:::_>`)
     29.   └─cli::cli_abort(...)
     30.     └─rlang::abort(...)
    
    [ FAIL 1 | WARN 10 | SKIP 56 | PASS 66 ]
    Error:
    ! Test failures.
    Execution halted

Package: eventglm
Check: examples
New result: ERROR
  Running examples in ‘eventglm-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: jackknife.competing.risks2
  > ### Title: Compute jackknife pseudo-observations of the cause-specific
  > ###   cumulative incidence for competing risks
  > ### Aliases: jackknife.competing.risks2
  > 
  > ### ** Examples
  > 
  > 
  > sfit.cuminc <- survival::survfit(survival::Surv(etime, event) ~ 1, data = mgus2)
  > mrs <- with(mgus2, Surv(etime, event))
  > pseudo.obs <- jackknife.competing.risks2(sfit.cuminc, times = 200, cause = "pcm", mrs)
  > mean(pseudo.obs)
  [1] 0.09190984
  > # agrees with
  > summary(sfit.cuminc, times = 200)
  Call: survfit(formula = survival::Surv(etime, event) ~ 1, data = mgus2)
  
  Error in cbind(mat, x$pstate) : 
    number of rows of matrices must match (see arg 2)
  Calls: <Anonymous> -> print.summary.survfitms -> cbind
  Execution halted

Package: JointAI
Check: for code/documentation mismatches
New result: WARNING
  Codoc mismatches from Rd file 'Surv.Rd':
  Surv
    Code: function(time, time2, event, type = c("right", "left",
                   "interval", "counting", "interval2"), origin = 0)
    Docs: function(time, time2, event, type = c("right", "left",
                   "interval", "counting", "interval2", "mstate"), origin
                   = 0)
    Mismatches in argument default values:
      Name: 'type' Code: c("right", "left", "interval", "counting", "interval2") Docs: c("right", "left", "interval", "counting", "interval2", "mstate")

Package: popEpi
Check: tests
New result: ERROR
    Running ‘testthat.R’ [68s/68s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > 
    > if (requireNamespace("testthat")) {
    +   library("testthat")
    +   library("popEpi")
    +   library("data.table")
    + 
    +   using_r_devel <- grepl(pattern = "devel", x = R.version$status)
    +   if (using_r_devel) {
    +     ## memory leak problem in data.table 1.11.2 in R-devel (3.6.0 atm)
    +     requireNamespace("data.table")
    +     data.table::setDTthreads(threads = 1L)
    +   }
    + 
    +   testthat::test_check("popEpi")
    + }
    Loading required namespace: testthat
    
    Attaching package: 'data.table'
    
    The following object is masked from 'package:base':
    
        %notin%
    
    Saving _problems/test_Surv-18.R
    NOTE: entry.status has been set to "DM" for all.
       first.bad.surv.int last.bad.surv.int surv.obs
                    <int>             <int>    <num>
    1:                 61               120      NaN
       first.bad.surv.int last.bad.surv.int surv.obs
                    <int>             <int>    <num>
    1:                 61               120      NaN
    Key: <agegr>
       agegr first.bad.surv.int last.bad.surv.int surv.obs
       <int>              <int>             <int>    <num>
    1:     3                 61               120      NaN
    Key: <agegr>
       agegr first.bad.surv.int last.bad.surv.int surv.obs
       <int>              <int>             <int>    <num>
    1:     3                 61               120      NaN
    [ FAIL 1 | WARN 0 | SKIP 41 | PASS 270 ]
    
    ══ Skipped tests (41) ══════════════════════════════════════════════════════════
    • Unit tests skipped normally (41): 'test_aggre.R:162:3', 'test_aggre.R:199:3',
      'test_expo.R:4:3', 'test_lexpand.R:5:3', 'test_lexpand.R:29:3',
      'test_lexpand.R:59:3', 'test_lexpand.R:78:3', 'test_lexpand.R:99:3',
      'test_lexpand.R:137:3', 'test_lexpand.R:213:3', 'test_lexpand.R:249:3',
      'test_lexpand.R:342:3', 'test_relpois_mean_curve.R:4:3', 'test_sir.R:221:5',
      'test_sir.R:257:3', 'test_splitLexisDT.R:4:3', 'test_splitMulti.R:9:3',
      'test_splitting_breaks.R:5:3', 'test_splitting_breaks.R:39:3',
      'test_splitting_randomly_on_fixed_data.R:9:3',
      'test_splitting_randomly_on_random_data.R:9:3', 'test_survmean.R:6:3',
      'test_survmean.R:76:3', 'test_survmean.R:117:3', 'test_survmean.R:166:3',
      'test_survmean.R:265:3', 'test_survtab_adjusted.R:4:3',
      'test_survtab_observed.R:67:3', 'test_survtab_relative.R:81:5',
      'test_survtab_usage.R:6:3', 'test_survtab_usage.R:121:3',
      'test_survtab_usage.R:198:3', 'test_survtab_usage.R:432:3',
      'test_utils.R:4:3', 'test_utils.R:27:3', 'test_utils.R:138:3',
      'test_utils.R:179:3', 'test_weighter.R:5:3', 'test_weighter.R:47:3',
      'test_weighter.R:99:3', 'test_weighter.R:122:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_Surv.R:15:3'): survival::Surv and popEpi::Surv's formals are in harmony ──
    Expected `popepi_formals` to be identical to `survival_formals`.
    Differences:
    Component "type": target, current do not match when deparsed
    
    [ FAIL 1 | WARN 0 | SKIP 41 | PASS 270 ]
    Error:
    ! Test failures.
    Execution halted

Package: rms
Check: for code/documentation mismatches
New result: WARNING
  Codoc mismatches from Rd file 'importexport.Rd':
  Surv
    Code: function(time, time2, event, type = c("right", "left",
                   "interval", "counting", "interval2"), origin = 0)
    Docs: function(time, time2, event, type = c("right", "left",
                   "interval", "counting", "interval2", "mstate"), origin
                   = 0)
    Mismatches in argument default values:
      Name: 'type' Code: c("right", "left", "interval", "counting", "interval2") Docs: c("right", "left", "interval", "counting", "interval2", "mstate")

Package: survSAKK
Check: tests
New result: ERROR
    Running ‘testthat.R’ [10s/10s]
  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(survSAKK)
    > 
    > test_check("survSAKK")
    Saving _problems/test-surv.plot-9.R
    Saving _problems/test-surv.plot-45.R
    Saving _problems/test-surv.plot-61.R
    Saving _problems/test-surv.plot-68.R
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    Saving _problems/test-surv.plot-260.R
    Saving _problems/test-surv.plot-272.R
    Saving _problems/test-surv.plot-281.R
    Saving _problems/test-surv.plot-291.R
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    Saving _problems/test-surv.plot-303.R
    Saving _problems/test-surv.plot-310.R
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    Saving _problems/test-surv.plot-330.R
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    Saving _problems/test-surv.plot-392.R
    Saving _problems/test-surv.plot-399.R
    Saving _problems/test-surv.plot-405.R
    Saving _problems/test-surv.plot-412.R
    Saving _problems/test-surv.plot-427.R
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    Saving _problems/test-surv.plot-473.R
    Saving _problems/test-surv.plot-479.R
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    Saving _problems/test-surv.plot-499.R
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    Saving _problems/test-surv.plot-604.R
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    Saving _problems/test-surv.plot-617.R
    Saving _problems/test-surv.plot-625.R
    [ FAIL 77 | WARN 17 | SKIP 0 | PASS 22 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-surv.plot.R:9:3'): surv.plot can plot without error ──────────
    Expected `surv.plot(fit = survObject)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:42:3'): surv.plot handles default color assignment ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:61:11'): Convert y unit into percent. ────────────
    Expected `surv.plot(fit = survObject, y.unit = "percent")` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:65:3'): Convert y unit into percent and check label ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:73:3'): Ensure `segment.quanitle` is handles without error. ──
    Expected `surv.plot(fit = survObject, segment.quantile = 0.5, segment.type = 1)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:77:3'): Ensure `segment.quanitle` is handles without error. ──
    Expected `surv.plot(fit = survObject, segment.quantile = 0.5, segment.type = 2)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:81:3'): Ensure `segment.quanitle` is handles without error. ──
    Expected `surv.plot(fit = survObject, segment.quantile = 0.5, segment.type = 3)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:85:3'): Ensure several `segment.quanitle` and different positions are handles without error. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:92:3'): Ensure several `segment.quanitle` and different positions are handles without error. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:99:3'): Ensure several `segment.quanitle` and different positions are handles without error. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:106:3'): Ensure `segment.timpoint` is handles without error. ──
    Expected `surv.plot(fit = survObject, segment.timepoint = 360, segment.type = 1)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:110:3'): Ensure `segment.timpoint` is handles without error. ──
    Expected `surv.plot(fit = survObject, segment.timepoint = 360, segment.type = 2)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:114:3'): Ensure `segment.timpoint` is handles without error. ──
    Expected `surv.plot(fit = survObject, segment.timepoint = 360, segment.type = 3)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:124:3'): surv.plot throws error for invalid risktable parameter ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:130:3'): surv.plot throws error for invalid risktable parameter ──
    Expected `surv.plot(fit = survObject, segment.timepoint = 0.5, segment.annotation = "left")` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:136:3'): surv.plot throws error for invalid risktable parameter ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:142:3'): surv.plot throws error for invalid risktable parameter ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:148:3'): surv.plot throws error for invalid risktable parameter ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:154:3'): surv.plot throws error for invalid risktable parameter ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:161:3'): Check if risktable colour can be modified ──
    Expected `surv.plot(fit = survObject, risktable.col = c("red", "yellow"))` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:170:3'): Ensure that legend can be modified manually ──
    Expected `surv.plot(fit = survObject, legend.name = "legend")` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:177:3'): Check logrank statistics ────────────────
    Expected `surv.plot(fit = survObject, stat = "logrank")` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:181:3'): Check coxph statistics ──────────────────
    Expected `surv.plot(fit = survObject, stat = "coxph", stat.position = "bottomleft")` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:185:3'): Check coxph_logrank statistics ──────────
    Expected `surv.plot(fit = survObject, stat = "coxph_logrank", stat.position = "topright")` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:189:3'): Check coxph_logrank statistics ──────────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:195:3'): Check if defined theme is executed ──────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:200:3'): Check if defined theme is executed ──────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:205:3'): Check if defined theme is executed ──────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:211:3'): Check if defined theme is executed ──────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:217:3'): Check if defined theme is executed ──────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:223:3'): Check if defined theme is executed ──────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:228:3'): Check if defined theme is executed ──────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:233:3'): Check if defined theme is executed ──────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:238:3'): Check if defined theme is executed ──────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:243:3'): Check if defined theme is executed ──────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:248:3'): Check if defined theme is executed ──────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:260:3'): Setting an invalid grid argument. ───────
    Expected `surv.plot(fit = survObject, grid = TRUE)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:272:3'): Check if risktable.title gives a valid output. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:281:3'): Check if conf.band.col gives a valid output. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:291:3'): Check if conf.band.col gives a valid output. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:295:3'): Check if conf.band.col gives a valid output. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:301:3'): Check if short annotation works without an error. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:307:3'): Check if short annotation works without an error for one arm with segment.main given. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:314:3'): Check if short annotation works without an error for more than two arms. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:321:3'): Check if short annotation works without an error. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:328:3'): Check if short annotation works without an error. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:334:3'): Check if CI for segment can be omitted for one arm ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:340:3'): Check for annotation with only one arm. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:346:3'): Check for annotation with only one arm. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:353:3'): Check for annotation with only one arm. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:359:3'): Check for annotation with only one arm. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:366:3'): Check for short annotation with only one arm and segment.main given. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:374:3'): Check for short annotation with more than two arms. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:381:3'): Check for short annotation with more than two arms in percent. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:389:3'): Check for annotation with only one arm. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:396:3'): Check for annotation with only one arm. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:403:3'): Check for annotation with only one arm. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:409:3'): Check for annotation with only one arm. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:425:3'): Check if CI with one arm can handle error. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:460:3'): Check if other quantile than median can be added. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:471:3'): Check several time points and position. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:477:3'): Check several time points and position. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:483:3'): Check several time points and position. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:489:3'): Check segment time point with short annotation with number of arms = 2. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:496:3'): Check that time point with short annotation works if arms != 2. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:503:3'): Check if time point label works for 'percent' and 'segment.main' given. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:511:3'): Check if time point label works for 'percent' and 'segment.main' not given. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:518:3'): Check segment time point with long annotation with number of arms = 2. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:560:3'): Check segment annotation if several segment timepoint are chosen and y.unit == 'percent'. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:568:3'): Check if `letter` on top left can be displayed. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:576:3'): Check segment Title if 'segment.main' was specified ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:590:3'): Check 'stat,position' = 'left'. ─────────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:596:3'): Check 'stat,position' = 'right'. ────────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:602:3'): Check 'stat,position' = 'bottomright'. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:608:3'): Check 'stat.position' = 'top'. ──────────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:614:3'): Check 'stat.fit' if 'reference.arm' is given. ──
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    ── Failure ('test-surv.plot.R:621:3'): Check 'risktable.col'. ──────────────────
    Expected `surv.plot(...)` to run silently.
    Actual noise: warnings.
    
    [ FAIL 77 | WARN 17 | SKIP 0 | PASS 22 ]
    Error:
    ! Test failures.
    Execution halted