Last updated on 2024-12-01 18:49:14 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.6.0 | 7.03 | 511.21 | 518.24 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.6.1 | 4.26 | 411.97 | 416.23 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.6.1 | 978.07 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.6.1 | 1032.81 | OK | |||
| r-devel-windows-x86_64 | 0.6.1 | 7.00 | 411.00 | 418.00 | OK | |
| r-patched-linux-x86_64 | 0.6.1 | 6.91 | 572.23 | 579.14 | OK | |
| r-release-linux-x86_64 | 0.5.2 | 4.35 | 435.70 | 440.05 | OK | |
| r-release-macos-arm64 | 0.6.1 | 215.00 | OK | |||
| r-release-macos-x86_64 | 0.6.1 | 353.00 | OK | |||
| r-release-windows-x86_64 | 0.6.1 | 9.00 | 430.00 | 439.00 | OK | |
| r-oldrel-macos-arm64 | 0.6.1 | 207.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.6.1 | 427.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.6.1 | 7.00 | 462.00 | 469.00 | OK |
Version: 0.6.0
Check: dependencies in R code
Result: WARN
Missing or unexported object: ‘visOmopResults::optionsVisOmopTable’
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.6.0
Check: examples
Result: ERROR
Running examples in ‘CohortSurvival-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optionsTableSurvival
> ### Title: Additional arguments for the function tableSurvival()
> ### Aliases: optionsTableSurvival
>
> ### ** Examples
>
> {
+ optionsTableSurvival()
+ }
Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.6.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [352s/272s]
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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.6.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a01_Single_event_of_interest.Rmd’ using rmarkdown
Quitting from lines 59-62 [unnamed-chunk-6] (a01_Single_event_of_interest.Rmd)
Error: processing vignette 'a01_Single_event_of_interest.Rmd' failed with diagnostics:
Can't select columns that don't exist.
✖ Column `result_type` doesn't exist.
--- failed re-building ‘a01_Single_event_of_interest.Rmd’
--- re-building ‘a02_Competing_risk_survival.Rmd’ using rmarkdown
Quitting from lines 56-65 [unnamed-chunk-5] (a02_Competing_risk_survival.Rmd)
Error: processing vignette 'a02_Competing_risk_survival.Rmd' failed with diagnostics:
Can't select columns that don't exist.
✖ Column `result_type` doesn't exist.
--- failed re-building ‘a02_Competing_risk_survival.Rmd’
--- re-building ‘a03_Further_survival_analyses.Rmd’ using rmarkdown
--- finished re-building ‘a03_Further_survival_analyses.Rmd’
SUMMARY: processing the following files failed:
‘a01_Single_event_of_interest.Rmd’ ‘a02_Competing_risk_survival.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang