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 ** Processing: /home/hornik/tmp/CRAN/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/CRAN/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 Package: CohortSurvival Check: tests New result: ERROR Running ‘testthat.R’ [53s/40s] 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 ───── 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) ``() 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 Package: flexsurv Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘standsurv.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN/flexsurv.Rcheck/vign_test/flexsurv/vignettes/standsurv_files/figure-html/unnamed-chunk-4-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 37313 bytes Input file size = 37439 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28394 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 = 28394 Output IDAT size = 28394 bytes (8919 bytes decrease) Output file size = 28472 bytes (8967 bytes = 23.95% decrease) ** Processing: /home/hornik/tmp/CRAN/flexsurv.Rcheck/vign_test/flexsurv/vignettes/standsurv_files/figure-html/unnamed-chunk-6-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 38920 bytes Input file size = 39046 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32388 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 = 32388 Output IDAT size = 32388 bytes (6532 bytes decrease) Output file size = 32466 bytes (6580 bytes = 16.85% decrease) ** Processing: /home/hornik/tmp/CRAN/flexsurv.Rcheck/vign_test/flexsurv/vignettes/standsurv_files/figure-html/unnamed-chunk-8-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 29139 bytes Input file size = 29253 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26043 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 = 26043 Output IDAT size = 26043 bytes (3096 bytes decrease) Output file size = 26121 bytes (3132 bytes = 10.71% decrease) ** Processing: /home/hornik/tmp/CRAN/flexsurv.Rcheck/vign_test/flexsurv/vignettes/standsurv_files/figure-html/unnamed-chunk-9-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 41148 bytes Input file size = 41286 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 34170 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 = 34170 Output IDAT size = 34170 bytes (6978 bytes decrease) Output file size = 34248 bytes (7038 bytes = 17.05% decrease) ** Processing: /home/hornik/tmp/CRAN/flexsurv.Rcheck/vign_test/flexsurv/vignettes/standsurv_files/figure-html/unnamed-chunk-10-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27208 bytes Input file size = 27322 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26525 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 IDAT size = 25481 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 = 5 IDAT size = 25481 Output IDAT size = 25481 bytes (1727 bytes decrease) Output file size = 25559 bytes (1763 bytes = 6.45% decrease) ** Processing: /home/hornik/tmp/CRAN/flexsurv.Rcheck/vign_test/flexsurv/vignettes/standsurv_files/figure-html/unnamed-chunk-11-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27752 bytes Input file size = 27866 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26653 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 IDAT size = 26063 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 = 5 IDAT size = 26063 Output IDAT size = 26063 bytes (1689 bytes decrease) Output file size = 26141 bytes (1725 bytes = 6.19% decrease) ** Processing: /home/hornik/tmp/CRAN/flexsurv.Rcheck/vign_test/flexsurv/vignettes/standsurv_files/figure-html/unnamed-chunk-12-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27014 bytes Input file size = 27128 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23968 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 = 23968 Output IDAT size = 23968 bytes (3046 bytes decrease) Output file size = 24046 bytes (3082 bytes = 11.36% decrease) ** Processing: /home/hornik/tmp/CRAN/flexsurv.Rcheck/vign_test/flexsurv/vignettes/standsurv_files/figure-html/unnamed-chunk-13-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22493 bytes Input file size = 22595 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21181 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 IDAT size = 20444 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 = 5 IDAT size = 20444 Output IDAT size = 20444 bytes (2049 bytes decrease) Output file size = 20522 bytes (2073 bytes = 9.17% decrease) ** Processing: /home/hornik/tmp/CRAN/flexsurv.Rcheck/vign_test/flexsurv/vignettes/standsurv_files/figure-html/unnamed-chunk-14-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 43374 bytes Input file size = 43512 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35839 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 = 35839 Output IDAT size = 35839 bytes (7535 bytes decrease) Output file size = 35917 bytes (7595 bytes = 17.45% decrease) ** Processing: /home/hornik/tmp/CRAN/flexsurv.Rcheck/vign_test/flexsurv/vignettes/standsurv_files/figure-html/unnamed-chunk-15-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 42594 bytes Input file size = 42732 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35099 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 = 35099 Output IDAT size = 35099 bytes (7495 bytes decrease) Output file size = 35177 bytes (7555 bytes = 17.68% decrease) ** Processing: /home/hornik/tmp/CRAN/flexsurv.Rcheck/vign_test/flexsurv/vignettes/standsurv_files/figure-html/unnamed-chunk-17-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 33497 bytes Input file size = 33623 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28646 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 = 28646 Output IDAT size = 28646 bytes (4851 bytes decrease) Output file size = 28724 bytes (4899 bytes = 14.57% decrease) ** Processing: /home/hornik/tmp/CRAN/flexsurv.Rcheck/vign_test/flexsurv/vignettes/standsurv_files/figure-html/unnamed-chunk-18-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 29256 bytes Input file size = 29370 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28078 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 IDAT size = 27665 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 = 5 IDAT size = 27665 Output IDAT size = 27665 bytes (1591 bytes decrease) Output file size = 27743 bytes (1627 bytes = 5.54% decrease) ** Processing: /home/hornik/tmp/CRAN/flexsurv.Rcheck/vign_test/flexsurv/vignettes/standsurv_files/figure-html/unnamed-chunk-20-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 37174 bytes Input file size = 37300 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31919 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 = 31919 Output IDAT size = 31919 bytes (5255 bytes decrease) Output file size = 31997 bytes (5303 bytes = 14.22% decrease) ** Processing: /home/hornik/tmp/CRAN/flexsurv.Rcheck/vign_test/flexsurv/vignettes/standsurv_files/figure-html/unnamed-chunk-20-2.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 33461 bytes Input file size = 33587 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32995 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 IDAT size = 31878 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 = 5 IDAT size = 31878 Output IDAT size = 31878 bytes (1583 bytes decrease) Output file size = 31956 bytes (1631 bytes = 4.86% decrease) ** Processing: /home/hornik/tmp/CRAN/flexsurv.Rcheck/vign_test/flexsurv/vignettes/standsurv_files/figure-html/unnamed-chunk-21-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 28166 bytes Input file size = 28280 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 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 IDAT size = 26705 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 = 5 IDAT size = 26705 Output IDAT size = 26705 bytes (1461 bytes decrease) Output file size = 26783 bytes (1497 bytes = 5.29% decrease) --- finished re-building ‘standsurv.Rmd’ --- re-building ‘flexsurv.Rnw’ using knitr --- finished re-building ‘flexsurv.Rnw’ --- re-building ‘multistate.Rnw’ using knitr Quitting from lines at lines 810-821 [unnamed-chunk-30] (multistate.Rnw) Error: processing vignette 'multistate.Rnw' failed with diagnostics: `cols` must select at least one column. --- failed re-building ‘multistate.Rnw’ --- re-building ‘distributions.Rnw’ using Sweave --- finished re-building ‘distributions.Rnw’ --- re-building ‘flexsurv-examples.Rnw’ using Sweave Loading required package: survival Forming integrated rmst function... Forming integrated mean function... Loading required package: TH.data Loading required package: MASS Attaching package: ‘TH.data’ The following object is masked from ‘package:MASS’: geyser --- finished re-building ‘flexsurv-examples.Rnw’ SUMMARY: processing the following file failed: ‘multistate.Rnw’ Error: Vignette re-building failed. Execution halted Package: ggfortify Check: tests New result: ERROR Running ‘test-all.R’ [17s/17s] Running the tests in ‘tests/test-all.R’ failed. Complete output: > library(testthat) > > suppressWarnings(RNGversion("3.5.0")) > set.seed(1, sample.kind = "Rejection") > > test_check('ggfortify') Loading required package: ggfortify Loading required package: ggplot2 [ FAIL 4 | WARN 12 | SKIP 48 | PASS 735 ] ══ Skipped tests (48) ══════════════════════════════════════════════════════════ • On CRAN (48): 'test-backcompat.R:2:3', 'test-base-infer.R:4:3', 'test-base-infer.R:17:3', 'test-base-infer.R:51:3', 'test-base.R:4:3', 'test-base.R:12:3', 'test-base_ts.R:4:3', 'test-basis.R:6:5', 'test-changepoint.R:4:3', 'test-changepoint.R:49:3', 'test-cluster.R:4:3', 'test-cluster.R:27:3', 'test-cluster.R:81:3', 'test-cluster.R:127:3', 'test-cluster.R:148:3', 'test-cluster.R:167:3', 'test-forecast.R:4:3', 'test-forecast.R:45:3', 'test-forecast.R:66:3', 'test-forecast.R:82:3', 'test-forecast.R:98:3', 'test-forecast.R:117:3', 'test-forecast.R:133:3', 'test-forecast.R:160:3', 'test-plotlib.R:4:3', 'test-plotlib.R:26:3', 'test-plotlib.R:98:3', 'test-plotlib.R:128:3', 'test-plotlib.R:150:3', 'test-plotlib.R:215:3', 'test-plotlib.R:226:3', 'test-stats-lm.R:7:3', 'test-stats-lm.R:27:3', 'test-stats-lm.R:40:3', 'test-stats-lm.R:202:3', 'test-stats-lm.R:363:3', 'test-stats-lm.R:526:3', 'test-stats-lm.R:546:3', 'test-stats-lm.R:561:3', 'test-stats-lm.R:570:3', 'test-stats.R:222:3', 'test-stats.R:319:3', 'test-stats.R:420:3', 'test-stats.R:495:3', 'test-stats.R:522:3', 'test-stats.R:582:3', 'test-stats.R:599:3', 'test-surv.R:238:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-surv.R:161:3'): fortify.survfit works for simple multistate data ── names(fortified) not equal to c(...). Lengths differ: 8 is not 9 ── Failure ('test-surv.R:164:3'): fortify.survfit works for simple multistate data ── dim(fortified) not equal to c(12, 9). 1/2 mismatches [2] 8 - 9 == -1 ── Failure ('test-surv.R:167:3'): fortify.survfit works for simple multistate data ── names(fortified) not equal to c(...). Lengths differ: 8 is not 9 ── Failure ('test-surv.R:170:3'): fortify.survfit works for simple multistate data ── dim(fortified) not equal to c(15, 9). 1/2 mismatches [2] 8 - 9 == -1 [ FAIL 4 | WARN 12 | SKIP 48 | PASS 735 ] Error: Test failures Execution halted Package: popEpi Check: tests New result: ERROR Running ‘testthat.R’ [66s/66s] 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 NOTE: entry.status has been set to "DM" for all. first.bad.surv.int last.bad.surv.int surv.obs 1: 61 120 NaN first.bad.surv.int last.bad.surv.int surv.obs 1: 61 120 NaN Key: agegr first.bad.surv.int last.bad.surv.int surv.obs 1: 3 61 120 NaN Key: agegr first.bad.surv.int last.bad.surv.int surv.obs 1: 3 61 120 NaN [ FAIL 2 | WARN 0 | SKIP 41 | PASS 269 ] ══ 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:52:3', 'test_survtab_relative.R:80:5', '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_survtab_observed.R:44:3'): surv.obs about the same as Kaplan-Meier & CIFs close to Aalen-Johansen ── cif$V1 not equal to st$CIF_canD. target is NULL, current is numeric ── Failure ('test_survtab_observed.R:45:3'): surv.obs about the same as Kaplan-Meier & CIFs close to Aalen-Johansen ── cif$V2 not equal to st$CIF_othD. target is NULL, current is numeric [ FAIL 2 | WARN 0 | SKIP 41 | PASS 269 ] Error: Test failures Execution halted