Last updated on 2024-05-02 04:01:00 CEST.
| Package | ERROR | OK |
|---|---|---|
| CodelistGenerator | 13 | |
| CohortSurvival | 7 | 6 |
| IncidencePrevalence | 13 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 7, OK: 6
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [80s/78s]
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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.4.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a01_Single_event_of_interest.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CohortSurvival.Rcheck/vign_test/CohortSurvival/vignettes/a01_Single_event_of_interest_files/figure-html/unnamed-chunk-7-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5693 bytes
Input file size = 6551 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5122
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5122
Output IDAT size = 5122 bytes (571 bytes decrease)
Output file size = 5200 bytes (1351 bytes = 20.62% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CohortSurvival.Rcheck/vign_test/CohortSurvival/vignettes/a01_Single_event_of_interest_files/figure-html/unnamed-chunk-10-1.png
768x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 61785 bytes
Input file size = 61947 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48898
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48898
Output IDAT size = 48898 bytes (12887 bytes decrease)
Output file size = 48976 bytes (12971 bytes = 20.94% decrease)
--- 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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [57s/71s]
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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.4.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a01_Single_event_of_interest.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CohortSurvival.Rcheck/vign_test/CohortSurvival/vignettes/a01_Single_event_of_interest_files/figure-html/unnamed-chunk-7-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5693 bytes
Input file size = 6551 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5122
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5122
Output IDAT size = 5122 bytes (571 bytes decrease)
Output file size = 5200 bytes (1351 bytes = 20.62% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CohortSurvival.Rcheck/vign_test/CohortSurvival/vignettes/a01_Single_event_of_interest_files/figure-html/unnamed-chunk-10-1.png
768x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 61785 bytes
Input file size = 61947 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48898
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48898
Output IDAT size = 48898 bytes (12887 bytes decrease)
Output file size = 48976 bytes (12971 bytes = 20.94% decrease)
--- 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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [67s/84s]
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 1 ]
══ 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:9:3'): mgus example: no Competing risk ──────
Error in `validateSummariseResult(x)`: ids are not unique in settings
Backtrace:
▆
1. ├─... %>% asSurvivalResult() at test-estimateSurvival.R:9:3
2. ├─CohortSurvival::asSurvivalResult(.)
3. │ └─omopgenerics::newSummarisedResult(result)
4. │ └─omopgenerics:::assertClass(x = x, class = "data.frame")
5. │ ├─base::paste0(...)
6. │ └─base::paste0(base::class(x), collapse = ", ")
7. └─CohortSurvival::estimateSingleEventSurvival(...)
8. └─omopgenerics::newSummarisedResult(surv_estimates)
9. └─omopgenerics:::validateSummariseResult(x)
10. └─cli::cli_abort("ids are not unique in settings")
11. └─rlang::abort(...)
[ FAIL 1 | WARN 0 | SKIP 45 | PASS 1 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.4.0
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 at lines 47-54 [unnamed-chunk-5] (a01_Single_event_of_interest.Rmd)
Error: processing vignette 'a01_Single_event_of_interest.Rmd' failed with diagnostics:
ids are not unique in settings
--- failed re-building ‘a01_Single_event_of_interest.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- 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 files failed:
‘a01_Single_event_of_interest.Rmd’ ‘a02_Competing_risk_survival.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-oldrel-windows-x86_64
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [65s/55s]
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 1 ]
══ 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:9:3'): mgus example: no Competing risk ──────
Error in `validateSummariseResult(x)`: ids are not unique in settings
Backtrace:
▆
1. ├─... %>% asSurvivalResult() at test-estimateSurvival.R:9:3
2. ├─CohortSurvival::asSurvivalResult(.)
3. │ └─omopgenerics::newSummarisedResult(result)
4. │ └─omopgenerics:::assertClass(x = x, class = "data.frame")
5. │ ├─base::paste0(...)
6. │ └─base::paste0(base::class(x), collapse = ", ")
7. └─CohortSurvival::estimateSingleEventSurvival(...)
8. └─omopgenerics::newSummarisedResult(surv_estimates)
9. └─omopgenerics:::validateSummariseResult(x)
10. └─cli::cli_abort("ids are not unique in settings")
11. └─rlang::abort(...)
[ FAIL 1 | WARN 0 | SKIP 45 | PASS 1 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [74s/61s]
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
Flavor: r-release-linux-x86_64
Version: 0.4.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a01_Single_event_of_interest.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortSurvival.Rcheck/vign_test/CohortSurvival/vignettes/a01_Single_event_of_interest_files/figure-html/unnamed-chunk-7-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5693 bytes
Input file size = 6551 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5122
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5122
Output IDAT size = 5122 bytes (571 bytes decrease)
Output file size = 5200 bytes (1351 bytes = 20.62% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortSurvival.Rcheck/vign_test/CohortSurvival/vignettes/a01_Single_event_of_interest_files/figure-html/unnamed-chunk-10-1.png
768x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 61785 bytes
Input file size = 61947 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48898
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48898
Output IDAT size = 48898 bytes (12887 bytes decrease)
Output file size = 48976 bytes (12971 bytes = 20.94% decrease)
--- 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
Flavor: r-release-linux-x86_64
Version: 0.4.0
Check: tests
Result: ERROR
Running 'testthat.R' [37s]
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
Flavor: r-release-windows-x86_64
Version: 0.4.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'a01_Single_event_of_interest.Rmd' using rmarkdown
--- 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
Flavor: r-release-windows-x86_64
Version: 0.4.0
Check: tests
Result: ERROR
Running 'testthat.R' [33s]
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 1 ]
══ 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:9:3'): mgus example: no Competing risk ──────
Error in `validateSummariseResult(x)`: ids are not unique in settings
Backtrace:
▆
1. ├─... %>% asSurvivalResult() at test-estimateSurvival.R:9:3
2. ├─CohortSurvival::asSurvivalResult(.)
3. │ └─omopgenerics::newSummarisedResult(result)
4. │ └─omopgenerics:::assertClass(x = x, class = "data.frame")
5. │ ├─base::paste0(...)
6. │ └─base::paste0(base::class(x), collapse = ", ")
7. └─CohortSurvival::estimateSingleEventSurvival(...)
8. └─omopgenerics::newSummarisedResult(surv_estimates)
9. └─omopgenerics:::validateSummariseResult(x)
10. └─cli::cli_abort("ids are not unique in settings")
11. └─rlang::abort(...)
[ FAIL 1 | WARN 0 | SKIP 45 | PASS 1 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64
Current CRAN status: OK: 13