* using log directory 'd:/Rcompile/CRANpkg/local/4.3/CohortSurvival.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'CohortSurvival/DESCRIPTION' ... OK
* this is package 'CohortSurvival' version '0.4.0'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CohortSurvival' can be installed ... OK
* checking installed package size ... 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s] OK
* checking loading without being on the library search path ... [1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [9s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... 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 ... [3s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [53s] ERROR
  Running 'testthat.R' [53s]
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 1 | WARN 0 | SKIP 45 | PASS 10 ]
  
  ══ Skipped tests (45) ══════════════════════════════════════════════════════════
  • On CRAN (45): 'test-benchmarkCohortSurvival.R:2:3',
    'test-benchmarkCohortSurvival.R:63:3', '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:567:3', 'test-addCohortSurvival.R:667:3',
    'test-addCohortSurvival.R:753:3', 'test-generateDeathCohort.R:2:3',
    'test-generateDeathCohort.R:62:3', 'test-generateDeathCohort.R:129:3',
    'test-generateDeathCohort.R:195:3', 'test-generateDeathCohort.R:262:3',
    'test-generateDeathCohort.R:351:3', 'test-generateDeathCohort.R:451:3',
    '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-tableSurvival.R:2:3',
    'test-tableSurvival.R:51:3', 'test-estimateSurvival.R:88:3',
    'test-estimateSurvival.R:127:3', 'test-estimateSurvival.R:177:3',
    'test-estimateSurvival.R:344:3', 'test-estimateSurvival.R:557:3',
    'test-estimateSurvival.R:708:3', 'test-estimateSurvival.R:1225:3',
    'test-estimateSurvival.R:1351:3', 'test-estimateSurvival.R:1373:3',
    'test-estimateSurvival.R:1408:3', 'test-estimateSurvival.R:1484:3',
    'test-estimateSurvival.R:1676:3', 'test-estimateSurvival.R:1800:3',
    'test-estimateSurvival.R:1830:3', 'test-estimateSurvival.R:1849:3',
    'test-estimateSurvival.R:1883:3', 'test-estimateSurvival.R:2014:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-estimateSurvival.R:43:3'): mgus example: no Competing risk ─────
  <vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
  Error in `dplyr::rename(., estimate = "V2")`: Can't rename columns that don't exist.
  x Column `V2` doesn't exist.
  Backtrace:
       ▆
    1. ├─... %>% asSurvivalResult() at test-estimateSurvival.R:43:3
    2. ├─CohortSurvival::asSurvivalResult(.)
    3. │ └─omopgenerics::newSummarisedResult(result)
    4. │   └─omopgenerics:::assertClass(x, "data.frame")
    5. │     ├─base::paste0(...)
    6. │     └─base::paste0(base::class(x), collapse = ", ")
    7. ├─CohortSurvival::estimateCompetingRiskSurvival(...)
    8. │ └─CohortSurvival:::estimateSurvival(...)
    9. │   └─CohortSurvival:::competingRiskSurvival(...)
   10. │     ├─... %>% ...
   11. │     ├─dplyr::bind_rows(...)
   12. │     │ └─rlang::list2(...)
   13. │     ├─dplyr::bind_cols(...)
   14. │     │ └─rlang::list2(...)
   15. │     └─... %>% dplyr::select("estimate")
   16. ├─dplyr::mutate(., strata_name = "overall", strata_level = "overall")
   17. ├─dplyr::mutate(., analysis_type = "competing_risk")
   18. ├─dplyr::mutate(...)
   19. ├─dplyr::select(., "estimate")
   20. ├─dplyr::rename(., estimate = "V2")
   21. ├─dplyr:::rename.data.frame(., estimate = "V2")
   22. │ └─tidyselect::eval_rename(expr(c(...)), .data)
   23. │   └─tidyselect:::rename_impl(...)
   24. │     └─tidyselect:::eval_select_impl(...)
   25. │       ├─tidyselect:::with_subscript_errors(...)
   26. │       │ └─base::withCallingHandlers(...)
   27. │       └─tidyselect:::vars_select_eval(...)
   28. │         └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   29. │           └─tidyselect:::eval_c(expr, data_mask, context_mask)
   30. │             └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   31. │               └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   32. │                 └─tidyselect:::as_indices_sel_impl(...)
   33. │                   └─tidyselect:::as_indices_impl(...)
   34. │                     └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
   35. │                       └─vctrs::vec_as_location(...)
   36. └─vctrs (local) `<fn>`()
   37.   └─vctrs:::stop_subscript_oob(...)
   38.     └─vctrs:::stop_subscript(...)
   39.       └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 45 | PASS 10 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [85s] ERROR
Error(s) in re-building vignettes:
--- re-building 'a01_Single_event_of_interest.Rmd' using rmarkdown
--- finished re-building 'a01_Single_event_of_interest.Rmd'

--- re-building 'a02_Competing_risk_survival.Rmd' using rmarkdown

Quitting from lines  at lines 55-64 [unnamed-chunk-5] (a02_Competing_risk_survival.Rmd)
Error: processing vignette 'a02_Competing_risk_survival.Rmd' failed with diagnostics:
Can't rename columns that don't exist.
✖ Column `V2` doesn't exist.
--- failed re-building 'a02_Competing_risk_survival.Rmd'

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
  'a02_Competing_risk_survival.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [17s] OK
* checking HTML version of manual ... [3s] OK
* DONE
Status: 2 ERRORs