CRAN Package Check Results for Maintainer ‘Edward Burn <edward.burn at ndorms.ox.ac.uk>’

Last updated on 2024-05-02 08:02:20 CEST.

Package	ERROR	OK
CodelistGenerator		13
CohortSurvival	7	6
IncidencePrevalence		13

Package CodelistGenerator

Current CRAN status: OK: 13

Package CohortSurvival

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’ [40s/43s] 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-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 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 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

Package IncidencePrevalence

Current CRAN status: OK: 13