Package check result: OK Changes to worse in reverse depends: Package: CodelistGenerator Check: tests New result: ERROR Running ‘testthat.R’ [193s/94s] 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(CodelistGenerator) > > test_check("CodelistGenerator") Starting 2 test processes [ FAIL 1 | WARN 444 | SKIP 22 | PASS 402 ] ══ Skipped tests (22) ══════════════════════════════════════════════════════════ • On CRAN (13): 'test-drugCodes.R:123:3', 'test-drugCodes.R:443:3', 'test-helperFunctions.R:2:3', 'test-helperFunctions.R:31:3', 'test-helperFunctions.R:46:3', 'test-helperFunctions.R:61:3', 'test-getCandidateCodes.R:310:3', 'test-summariseCodeUse.R:2:1', 'test-summariseCodeUse.R:295:3', 'test-tableAchillesCodeUse.R:2:3', 'test-tableAchillesCodeUse.R:65:3', 'test-tableCodeUse.R:2:3', 'test-tableCodeUse.R:96:3' • Sys.getenv("CDM5_POSTGRESQL_DBNAME") == "" is TRUE (1): 'test-dbms.R:306:3' • Sys.getenv("CDM5_REDSHIFT_DBNAME") == "" is TRUE (4): 'test-codesFrom.R:131:3', 'test-dbms.R:5:3', 'test-findUnmappedCodes.R:3:3', 'test-summariseCodeUse.R:492:3' • Sys.getenv("CDM5_SQL_SERVER_SERVER") == "" is TRUE (2): 'test-codesInUse.R:36:3', 'test-dbms.R:458:3' • Sys.getenv("SNOWFLAKE_SERVER") == "" is TRUE (1): 'test-dbms.R:168:3' • Sys.getenv("darwinDbDatabaseServer") == "" is TRUE (1): 'test-synthea_sql_server.R:2:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-summariseAchillesCodeUse.R:28:3'): achilles code use ───────── all(...) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 1 | WARN 444 | SKIP 22 | PASS 402 ] Error: Test failures Execution halted Package: CohortCharacteristics Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘summarise_characteristics.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Quitting from lines 76-83 [unnamed-chunk-5] (summarise_characteristics.Rmd) Error: processing vignette 'summarise_characteristics.Rmd' failed with diagnostics: argument "x" is missing, with no default --- failed re-building ‘summarise_characteristics.Rmd’ --- re-building ‘summarise_cohort_overlap.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Quitting from lines 79-80 [unnamed-chunk-4] (summarise_cohort_overlap.Rmd) Error: processing vignette 'summarise_cohort_overlap.Rmd' failed with diagnostics: unused argument (formatEstimateName = c(`N (%)` = " (%)")) --- failed re-building ‘summarise_cohort_overlap.Rmd’ --- re-building ‘summarise_cohort_timing.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Quitting from lines 81-87 [unnamed-chunk-5] (summarise_cohort_timing.Rmd) Error: processing vignette 'summarise_cohort_timing.Rmd' failed with diagnostics: argument "x" is missing, with no default --- failed re-building ‘summarise_cohort_timing.Rmd’ --- re-building ‘summarise_large_scale_characteristics.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘summarise_large_scale_characteristics.Rmd’ SUMMARY: processing the following files failed: ‘summarise_characteristics.Rmd’ ‘summarise_cohort_overlap.Rmd’ ‘summarise_cohort_timing.Rmd’ Error: Vignette re-building failed. Execution halted Package: CohortCharacteristics Check: tests New result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [265s/163s] 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(CohortCharacteristics) > > test_check("CohortCharacteristics") Starting 2 test processes [ FAIL 1 | WARN 0 | SKIP 15 | PASS 161 ] ══ Skipped tests (15) ══════════════════════════════════════════════════════════ • On CRAN (15): 'test-plotCharacteristics.R:2:3', 'test-plotCharacteristics.R:136:3', 'test-plotCohortOverlap.R:2:3', 'test-plotCohortTiming.R:2:3', 'test-plotCohortTiming.R:94:3', 'test-plotLargeScaleCharacteristics.R:3:3', 'test-summariseCohortCount.R:2:3', 'test-summariseLargeScaleCharacteristics.R:2:3', 'test-tableCharacteristics.R:2:3', 'test-tableCharacteristics.R:123:3', 'test-tableCohortOverlap.R:2:3', 'test-tableCohortTiming.R:2:3', 'test-tableLargeScaleCharacteristics.R:2:3', 'test-summariseCharacteristics.R:1162:3', 'test-summariseCharacteristics.R:1392:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-summariseCohortTiming.R:51:3'): summariseCohortTiming ──────── omopgenerics::settings(timing1)$restrict_to_first_entry is not TRUE `actual` is a character vector ('TRUE') `expected` is a logical vector (TRUE) [ FAIL 1 | WARN 0 | SKIP 15 | PASS 161 ] Error: Test failures Execution halted Package: CohortConstructor Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘a00_introduction.Rmd’ using rmarkdown --- finished re-building ‘a00_introduction.Rmd’ --- re-building ‘a01_building_base_cohorts.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a01_building_base_cohorts.Rmd’ --- re-building ‘a02_cohort_table_requirements.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB ** Processing: /home/hornik/tmp/CRAN_recheck/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a02_cohort_table_requirements_files/figure-html/unnamed-chunk-15-1.png 288x288 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3779 bytes Input file size = 4634 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3377 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 = 3377 Output IDAT size = 3377 bytes (402 bytes decrease) Output file size = 3455 bytes (1179 bytes = 25.44% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a02_cohort_table_requirements_files/figure-html/unnamed-chunk-16-1.png 288x288 pixels, 8 bits/pixel, 252 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3614 bytes Input file size = 4460 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3284 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 = 3284 Output IDAT size = 3284 bytes (330 bytes decrease) Output file size = 3362 bytes (1098 bytes = 24.62% decrease) --- finished re-building ‘a02_cohort_table_requirements.Rmd’ --- re-building ‘a03_require_demographics.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a03_require_demographics.Rmd’ --- re-building ‘a04_require_intersections.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a04_require_intersections.Rmd’ --- re-building ‘a05_update_cohort_start_end.Rmd’ using rmarkdown --- finished re-building ‘a05_update_cohort_start_end.Rmd’ --- re-building ‘a06_concatanate_cohorts.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a06_concatanate_cohorts.Rmd’ --- re-building ‘a07_filter_cohorts.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a07_filter_cohorts.Rmd’ --- re-building ‘a08_split_cohorts.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a08_split_cohorts.Rmd’ --- re-building ‘a09_combine_cohorts.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a09_combine_cohorts.Rmd’ --- re-building ‘a10_match_cohorts.Rmd’ using rmarkdown --- finished re-building ‘a10_match_cohorts.Rmd’ --- re-building ‘a11_benchmark.Rmd’ using rmarkdown Quitting from lines 124-137 [unnamed-chunk-5] (a11_benchmark.Rmd) Error: processing vignette 'a11_benchmark.Rmd' failed with diagnostics: The size of `nm` (2) must be compatible with the size of `x` (0). --- failed re-building ‘a11_benchmark.Rmd’ SUMMARY: processing the following file failed: ‘a11_benchmark.Rmd’ Error: Vignette re-building failed. Execution halted Package: CohortSurvival Check: dependencies in R code New result: WARNING Missing or unexported object: ‘visOmopResults::optionsVisOmopTable’ Package: CohortSurvival Check: examples New result: ERROR Running examples in ‘CohortSurvival-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: optionsTableSurvival > ### Title: Additional arguments for the function tableSurvival() > ### Aliases: optionsTableSurvival > > ### ** Examples > > { + optionsTableSurvival() + } Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' Execution halted 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 Quitting from lines 59-62 [unnamed-chunk-6] (a01_Single_event_of_interest.Rmd) Error: processing vignette 'a01_Single_event_of_interest.Rmd' failed with diagnostics: Can't select columns that don't exist. ✖ Column `result_type` doesn't exist. --- failed re-building ‘a01_Single_event_of_interest.Rmd’ --- re-building ‘a02_Competing_risk_survival.Rmd’ using rmarkdown Quitting from lines 56-65 [unnamed-chunk-5] (a02_Competing_risk_survival.Rmd) Error: processing vignette 'a02_Competing_risk_survival.Rmd' failed with diagnostics: Can't select columns that don't exist. ✖ Column `result_type` doesn't exist. --- failed re-building ‘a02_Competing_risk_survival.Rmd’ --- re-building ‘a03_Further_survival_analyses.Rmd’ using rmarkdown --- finished re-building ‘a03_Further_survival_analyses.Rmd’ SUMMARY: processing the following files failed: ‘a01_Single_event_of_interest.Rmd’ ‘a02_Competing_risk_survival.Rmd’ Error: Vignette re-building failed. Execution halted Package: CohortSurvival Check: tests New result: ERROR Running ‘testthat.R’ [217s/151s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(CohortSurvival) > > test_check("CohortSurvival") Starting 2 test processes [ FAIL 4 | WARN 47 | SKIP 48 | PASS 15 ] ══ Skipped tests (48) ══════════════════════════════════════════════════════════ • On CRAN (48): 'test-deathDiagnostics.R:2:3', 'test-deathDiagnostics.R:116:3', 'test-addCohortSurvival.R:71:3', 'test-addCohortSurvival.R:158:3', 'test-addCohortSurvival.R:271:3', 'test-addCohortSurvival.R:377:3', 'test-addCohortSurvival.R:489:3', 'test-addCohortSurvival.R:575:3', 'test-addCohortSurvival.R:675:3', 'test-addCohortSurvival.R:762:3', 'test-generateDeathCohort.R:2:3', 'test-generateDeathCohort.R:61:3', 'test-generateDeathCohort.R:128:3', 'test-generateDeathCohort.R:194:3', 'test-generateDeathCohort.R:261:3', 'test-generateDeathCohort.R:349:3', 'test-generateDeathCohort.R:449:3', 'test-mockMGUS2cdm.R:2:3', 'test-plotSurvival.R:2:3', 'test-plotSurvival.R:19:3', 'test-plotSurvival.R:37:3', 'test-plotSurvival.R:57:3', 'test-plotSurvival.R:77:3', 'test-plotSurvival.R:98:3', 'test-plotSurvival.R:129:3', 'test-plotSurvival.R:149:3', 'test-plotSurvival.R:172:3', 'test-plotSurvival.R:191:3', 'test-tableSurvival.R:2:3', 'test-tableSurvival.R:88:3', 'test-estimateSurvival.R:87:3', 'test-estimateSurvival.R:126:3', 'test-estimateSurvival.R:176:3', 'test-estimateSurvival.R:343:3', 'test-estimateSurvival.R:556:3', 'test-estimateSurvival.R:707:3', 'test-estimateSurvival.R:1224:3', 'test-estimateSurvival.R:1350:3', 'test-estimateSurvival.R:1372:3', 'test-estimateSurvival.R:1448:3', 'test-estimateSurvival.R:1640:3', 'test-estimateSurvival.R:1763:3', 'test-estimateSurvival.R:1793:3', 'test-estimateSurvival.R:1812:3', 'test-estimateSurvival.R:1846:3', 'test-estimateSurvival.R:1979:3', 'test-estimateSurvival.R:2106:3', 'test-estimateSurvival.R:2216:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-reexports-omopgenerics.R:17:3'): omopgenerics reexports work ── Expected `tableSurvival(surv_imported, type = "tibble")` to run without any errors. i Actually got a with text: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' ── Failure ('test-reexports-omopgenerics.R:30:3'): omopgenerics reexports work ── isTRUE(all.equal(surv, surv_nosup, check.attributes = FALSE)) is not FALSE `actual`: TRUE `expected`: FALSE ── Failure ('test-reexports-omopgenerics.R:34:3'): omopgenerics reexports work ── isTRUE(all.equal(surv, surv_nosup_imported, check.attributes = FALSE)) is not TRUE `actual`: FALSE `expected`: TRUE ── Error ('test-estimateSurvival.R:9:3'): mgus example: no Competing risk ────── Error in `dplyr::select(., c("cdm_name", "group_name", "group_level", "strata_name", "strata_level", "variable_name", "variable_level", "estimate_name", "estimate_type", "estimate_value", "additional_name", "additional_level", "result_type", "outcome", "competing_outcome", "eventgap"))`: Can't select columns that don't exist. x Column `result_type` doesn't exist. Backtrace: ▆ 1. ├─... %>% asSurvivalResult() at test-estimateSurvival.R:9:3 2. ├─CohortSurvival::asSurvivalResult(.) 3. │ └─... %>% ... 4. ├─dplyr::mutate(., estimate_value = as.numeric(.data$estimate_value)) 5. ├─visOmopResults::splitGroup(.) 6. │ └─omopgenerics:::splitNameLevelInternal(...) 7. │ └─omopgenerics::assertTable(...) 8. │ ├─omopgenerics:::checkDistinct(...) 9. │ ├─omopgenerics:::checkColumns2(...) 10. │ ├─omopgenerics:::checkNumberRows(...) 11. │ ├─omopgenerics:::checkNumberColumns(...) 12. │ ├─omopgenerics:::checkClass(...) 13. │ ├─omopgenerics:::checkNull(createCheckObject(x), null) 14. │ └─omopgenerics:::createCheckObject(x) 15. ├─visOmopResults::splitAdditional(.) 16. │ └─omopgenerics:::splitNameLevelInternal(...) 17. │ └─omopgenerics::assertTable(...) 18. │ ├─omopgenerics:::checkDistinct(...) 19. │ ├─omopgenerics:::checkColumns2(...) 20. │ ├─omopgenerics:::checkNumberRows(...) 21. │ ├─omopgenerics:::checkNumberColumns(...) 22. │ ├─omopgenerics:::checkClass(...) 23. │ ├─omopgenerics:::checkNull(createCheckObject(x), null) 24. │ └─omopgenerics:::createCheckObject(x) 25. ├─dplyr::select(...) 26. ├─dplyr:::select.data.frame(...) 27. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call) 28. │ └─tidyselect:::eval_select_impl(...) 29. │ ├─tidyselect:::with_subscript_errors(...) 30. │ │ └─base::withCallingHandlers(...) 31. │ └─tidyselect:::vars_select_eval(...) 32. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask) 33. │ └─tidyselect:::eval_c(expr, data_mask, context_mask) 34. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init) 35. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask) 36. │ └─tidyselect:::eval_c(expr, data_mask, context_mask) 37. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init) 38. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask) 39. │ └─tidyselect:::as_indices_sel_impl(...) 40. │ └─tidyselect:::as_indices_impl(...) 41. │ └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg) 42. │ └─vctrs::vec_as_location(...) 43. └─vctrs (local) ``() 44. └─vctrs:::stop_subscript_oob(...) 45. └─vctrs:::stop_subscript(...) 46. └─rlang::abort(...) [ FAIL 4 | WARN 47 | SKIP 48 | PASS 15 ] Error: Test failures Execution halted Package: CohortSymmetry Check: dependencies in R code New result: WARNING Missing or unexported objects: ‘visOmopResults::fxTable’ ‘visOmopResults::gtTable’ ‘visOmopResults::splitNameLevel’ Package: CohortSymmetry Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘a01_Introduction.Rmd’ using rmarkdown Quitting from lines 102-107 [unnamed-chunk-6] (a01_Introduction.Rmd) Error: processing vignette 'a01_Introduction.Rmd' failed with diagnostics: 'splitNameLevel' is not an exported object from 'namespace:visOmopResults' --- failed re-building ‘a01_Introduction.Rmd’ --- re-building ‘a02_Generate_a_sequence_cohort.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a02_Generate_a_sequence_cohort.Rmd’ --- re-building ‘a03_Summarise_sequence_ratios.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a03_Summarise_sequence_ratios.Rmd’ --- re-building ‘a04_Visualise_sequence_ratios.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Quitting from lines 83-84 [unnamed-chunk-5] (a04_Visualise_sequence_ratios.Rmd) Error: processing vignette 'a04_Visualise_sequence_ratios.Rmd' failed with diagnostics: unused argument (estimateNameFormat = estimateNameFormat) --- failed re-building ‘a04_Visualise_sequence_ratios.Rmd’ --- re-building ‘a05_Summarise_temporal_symmetry.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a05_Summarise_temporal_symmetry.Rmd’ --- re-building ‘a06_Visualise_temporal_symmetry.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Quitting from lines 82-83 [unnamed-chunk-5] (a06_Visualise_temporal_symmetry.Rmd) Error: processing vignette 'a06_Visualise_temporal_symmetry.Rmd' failed with diagnostics: 'splitNameLevel' is not an exported object from 'namespace:visOmopResults' --- failed re-building ‘a06_Visualise_temporal_symmetry.Rmd’ SUMMARY: processing the following files failed: ‘a01_Introduction.Rmd’ ‘a04_Visualise_sequence_ratios.Rmd’ ‘a06_Visualise_temporal_symmetry.Rmd’ Error: Vignette re-building failed. Execution halted Package: CohortSymmetry Check: tests New result: ERROR Running ‘testthat.R’ [169s/161s] 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/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(CohortSymmetry) > > test_check("CohortSymmetry") Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable', target signature 'duckdb_connection#Id'. "duckdb_connection#ANY" would also be valid `days_prior_observation` casted to character. `group` is not present in settings. `days_prior_observation` casted to character. `days_prior_observation` casted to character. -- 1 combination of 4 had index always before marker `days_prior_observation` casted to character. -- 1 combination of 4 had index always before marker `days_prior_observation` casted to character. Joining with `by = join_by(result_id, cdm_name)` `days_prior_observation` casted to character. Joining with `by = join_by(result_id, cdm_name)` `days_prior_observation` casted to character. `days_prior_observation` casted to character. `days_prior_observation` casted to character. [ FAIL 3 | WARN 73 | SKIP 53 | PASS 41 ] ══ Skipped tests (53) ══════════════════════════════════════════════════════════ • On CRAN (53): 'test-attrition.R:2:3', 'test-attrition.R:63:3', 'test-attrition.R:149:3', 'test-attrition.R:310:3', 'test-attrition.R:397:3', 'test-attrition.R:461:3', 'test-attrition.R:592:3', 'test-attrition.R:769:3', 'test-displayTable.R:30:3', 'test-displayTable.R:58:3', 'test-displayTable.R:86:3', 'test-eunomia.R:2:3', 'test-eunomia.R:65:3', 'test-generateSequenceCohortSet.R:3:3', 'test-generateSequenceCohortSet.R:20:3', 'test-generateSequenceCohortSet.R:96:3', 'test-generateSequenceCohortSet.R:153:3', 'test-generateSequenceCohortSet.R:205:3', 'test-generateSequenceCohortSet.R:259:3', 'test-generateSequenceCohortSet.R:288:3', 'test-generateSequenceCohortSet.R:330:3', 'test-generateSequenceCohortSet.R:356:3', 'test-generateSequenceCohortSet.R:427:3', 'test-generateSequenceCohortSet.R:515:3', 'test-generateSequenceCohortSet.R:663:3', 'test-generateSequenceCohortSet.R:751:3', 'test-generateSequenceCohortSet.R:764:3', 'test-generateSequenceCohortSet.R:776:3', 'test-generateSequenceCohortSet.R:788:3', 'test-generateSequenceCohortSet.R:800:3', 'test-generateSequenceCohortSet.R:818:3', 'test-generateSequenceCohortSet.R:836:3', 'test-generateSequenceCohortSet.R:848:3', 'test-generateSequenceCohortSet.R:859:3', 'test-generateSequenceCohortSet.R:870:3', 'test-generateSequenceCohortSet.R:894:3', 'test-plotSequenceRatio.R:41:3', 'test-plotSequenceRatio.R:85:3', 'test-plotTemporalSymmetry.R:42:3', 'test-plotTemporalSymmetry.R:86:3', 'test-summariseSequenceRatios.R:203:3', 'test-summariseSequenceRatios.R:415:3', 'test-summariseSequenceRatios.R:522:3', 'test-summariseSequenceRatios.R:604:3', 'test-summariseSequenceRatios.R:763:3', 'test-summariseSequenceRatios.R:801:3', 'test-summariseSequenceRatios.R:839:3', 'test-summariseSequenceRatios.R:877:3', 'test-summariseTemporalSymmetry.R:73:3', 'test-summariseTemporalSymmetry.R:98:3', 'test-summariseTemporalSymmetry.R:156:3', 'test-test-dbs.R:2:3', 'test-test-dbs.R:50:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-displayTable.R:14:3'): tableSequenceRatios - gt output ───────── Error in `visOmopResults::formatEstimateName(visOmopResults::formatEstimateValue(result, decimals = .options$decimals, decimalMark = .options$decimalMark, bigMark = .options$bigMark), estimateNameFormat = estimateNameFormat, keepNotFormatted = .options$keepNotFormatted, useFormatOrder = .options$useFormatOrder)`: unused argument (estimateNameFormat = estimateNameFormat) Backtrace: ▆ 1. └─CohortSymmetry::tableSequenceRatios(res) at test-displayTable.R:14:3 2. ├─dplyr::select(...) 3. ├─tidyr::pivot_wider(...) 4. ├─dplyr::mutate(...) 5. ├─dplyr::rename(...) 6. ├─... %>% ... 7. ├─dplyr::select(...) 8. ├─dplyr::mutate(...) 9. ├─dplyr::select(...) 10. └─visOmopResults::splitGroup(...) 11. └─omopgenerics:::splitNameLevelInternal(...) 12. └─omopgenerics::assertTable(...) 13. ├─omopgenerics:::checkDistinct(...) 14. ├─omopgenerics:::checkColumns2(...) 15. ├─omopgenerics:::checkNumberRows(...) 16. ├─omopgenerics:::checkNumberColumns(...) 17. ├─omopgenerics:::checkClass(...) 18. ├─omopgenerics:::checkNull(createCheckObject(x), null) 19. └─omopgenerics:::createCheckObject(x) ── Error ('test-plotTemporalSymmetry.R:25:3'): plot working ──────────────────── Error: 'splitNameLevel' is not an exported object from 'namespace:visOmopResults' Backtrace: ▆ 1. └─CohortSymmetry::plotTemporalSymmetry(result = result) at test-plotTemporalSymmetry.R:25:3 2. ├─dplyr::compute(...) 3. ├─dplyr::mutate(...) 4. ├─dplyr::mutate(...) 5. ├─dplyr::mutate(...) 6. ├─dplyr::filter(...) 7. ├─dplyr::rename(...) 8. ├─dplyr::ungroup(...) 9. ├─dplyr::select(...) 10. ├─tidyr::pivot_wider(...) 11. ├─tidyr::pivot_wider(...) 12. ├─dplyr::mutate(...) 13. ├─dplyr::group_by(...) 14. └─dplyr::select(...) ── Failure ('test-summariseTemporalSymmetry.R:30:3'): test summariseTemporalSymmetry ── is.na(unique(temporal_symmetry$estimate_value)) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 3 | WARN 73 | SKIP 53 | PASS 41 ] Error: Test failures Execution halted Package: DrugUtilisation Check: dependencies in R code New result: WARNING Missing or unexported object: ‘visOmopResults::optionsVisOmopTable’ Package: DrugUtilisation Check: examples New result: ERROR Running examples in ‘DrugUtilisation-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: defaultTableOptions > ### Title: Additional arguments for the table functions. > ### Aliases: defaultTableOptions > > ### ** Examples > > { + defaultTableOptions() + } Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' Execution halted Package: DrugUtilisation Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘create_cohorts.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-9-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24762 bytes Input file size = 24876 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20566 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 = 20566 Output IDAT size = 20566 bytes (4196 bytes decrease) Output file size = 20644 bytes (4232 bytes = 17.01% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-10-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3638 bytes Input file size = 4364 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3050 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3032 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 = 1 f = 0 IDAT size = 3032 Output IDAT size = 3032 bytes (606 bytes decrease) Output file size = 3758 bytes (606 bytes = 13.89% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-11-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3617 bytes Input file size = 4343 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3032 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3011 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 = 1 f = 0 IDAT size = 3011 Output IDAT size = 3011 bytes (606 bytes decrease) Output file size = 3737 bytes (606 bytes = 13.95% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-12-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3563 bytes Input file size = 4289 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2989 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2969 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 = 1 f = 0 IDAT size = 2969 Output IDAT size = 2969 bytes (594 bytes decrease) Output file size = 3695 bytes (594 bytes = 13.85% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-42-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11056 bytes Input file size = 11146 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8629 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 = 8629 Output IDAT size = 8629 bytes (2427 bytes decrease) Output file size = 8707 bytes (2439 bytes = 21.88% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-43-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7942 bytes Input file size = 8020 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6505 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 = 6505 Output IDAT size = 6505 bytes (1437 bytes decrease) Output file size = 6583 bytes (1437 bytes = 17.92% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-44-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7940 bytes Input file size = 8018 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6533 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 = 6533 Output IDAT size = 6533 bytes (1407 bytes decrease) Output file size = 6611 bytes (1407 bytes = 17.55% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-45-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7777 bytes Input file size = 7855 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6351 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 = 6351 Output IDAT size = 6351 bytes (1426 bytes decrease) Output file size = 6429 bytes (1426 bytes = 18.15% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-46-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7789 bytes Input file size = 7867 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6381 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 = 6381 Output IDAT size = 6381 bytes (1408 bytes decrease) Output file size = 6459 bytes (1408 bytes = 17.90% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-47-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7432 bytes Input file size = 7510 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6162 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 = 6162 Output IDAT size = 6162 bytes (1270 bytes decrease) Output file size = 6240 bytes (1270 bytes = 16.91% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-48-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7445 bytes Input file size = 7523 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6182 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 = 6182 Output IDAT size = 6182 bytes (1263 bytes decrease) Output file size = 6260 bytes (1263 bytes = 16.79% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-49-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7940 bytes Input file size = 8018 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6533 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 = 6533 Output IDAT size = 6533 bytes (1407 bytes decrease) Output file size = 6611 bytes (1407 bytes = 17.55% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-50-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8705 bytes Input file size = 8795 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7098 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 = 7098 Output IDAT size = 7098 bytes (1607 bytes decrease) Output file size = 7176 bytes (1619 bytes = 18.41% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-51-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8332 bytes Input file size = 8422 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6889 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 = 6889 Output IDAT size = 6889 bytes (1443 bytes decrease) Output file size = 6967 bytes (1455 bytes = 17.28% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-52-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8356 bytes Input file size = 8446 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6922 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 = 6922 Output IDAT size = 6922 bytes (1434 bytes decrease) Output file size = 7000 bytes (1446 bytes = 17.12% decrease) --- finished re-building ‘create_cohorts.Rmd’ --- re-building ‘drug_utilisation.Rmd’ using rmarkdown Quitting from lines 277-278 [unnamed-chunk-9] (drug_utilisation.Rmd) Error: processing vignette 'drug_utilisation.Rmd' failed with diagnostics: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' --- failed re-building ‘drug_utilisation.Rmd’ SUMMARY: processing the following file failed: ‘drug_utilisation.Rmd’ Error: Vignette re-building failed. Execution halted Package: DrugUtilisation Check: tests New result: ERROR Running ‘testthat.R’ [180s/97s] 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(DrugUtilisation) > > test_check("DrugUtilisation") Starting 2 test processes [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] ══ Skipped tests (50) ══════════════════════════════════════════════════════════ • On CRAN (50): 'test-addDrugUtilisation.R:3:3', 'test-addDrugUtilisation.R:156:3', 'test-addDrugUtilisation.R:196:3', 'test-benchmarkDrugUtilisation.R:2:3', 'test-dailyDose.R:2:3', 'test-generateDrugUtilisationCohortSet.R:2:3', 'test-generateDrugUtilisationCohortSet.R:23:3', 'test-generatedAtcCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:39:3', 'test-generatedIngredientCohortSet.R:54:3', 'test-generatedIngredientCohortSet.R:69:3', 'test-generatedIngredientCohortSet.R:98:3', 'test-drugUse.R:2:3', 'test-drugUse.R:42:3', 'test-drugUse.R:259:3', 'test-drugUse.R:463:3', 'test-drugUse.R:608:3', 'test-drugUse.R:860:3', 'test-drugUse.R:883:3', 'test-drugUse.R:932:3', 'test-drugUse.R:967:3', 'test-drugUse.R:1025:3', 'test-patterns.R:2:3', 'test-plotProportionOfPatientsCovered.R:2:3', 'test-plotProportionOfPatientsCovered.R:58:3', 'test-plotProportionOfPatientsCovered.R:100:3', 'test-plotTreatment.R:2:3', 'test-plots.R:2:3', 'test-readConceptList.R:2:3', 'test-require.R:2:3', 'test-require.R:143:3', 'test-require.R:324:3', 'test-require.R:432:3', 'test-require.R:526:3', 'test-require.R:597:3', 'test-indication.R:2:3', 'test-indication.R:202:3', 'test-indication.R:364:3', 'test-indication.R:481:3', 'test-summariseProportionOfPatientsCovered.R:94:3', 'test-summariseProportionOfPatientsCovered.R:170:3', 'test-summariseProportionOfPatientsCovered.R:277:3', 'test-summariseProportionOfPatientsCovered.R:497:3', 'test-summariseProportionOfPatientsCovered.R:550:3', 'test-tables.R:2:3', 'test-tables.R:132:3', 'test-tables.R:271:3', 'test-tables.R:393:3', 'test-tables.R:502:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-summariseDrugRestart.R:76:3'): summarise drug restart ──────── is.na(settings(resultsCohort)$censor_date) is not TRUE `actual`: `expected`: TRUE ── Failure ('test-summariseDrugRestart.R:83:3'): summarise drug restart ──────── unique(resultsSup$estimate_value) (`actual`) not equal to c(NA_character_, "0") (`expected`). `actual`: "-" "0" `expected`: NA "0" ── Failure ('test-summariseTreatment.R:49:3'): test summariseTreatment ───────── all(...) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-summariseDrugUtilisation.R:65:3'): summariseDrugUtilisation works ── all(...) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] Error: Test failures Execution halted Package: IncidencePrevalence Check: dependencies in R code New result: WARNING Missing or unexported object: ‘visOmopResults::optionsVisOmopTable’ Package: IncidencePrevalence Check: examples New result: ERROR Running examples in ‘IncidencePrevalence-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: optionsTableIncidence > ### Title: Additional arguments for the functions tableIncidence. > ### Aliases: optionsTableIncidence > > ### ** Examples > > { + optionsTableIncidence() + } Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' Execution halted Package: IncidencePrevalence Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence_files/figure-html/unnamed-chunk-10-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 31155 bytes Input file size = 31269 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26287 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 = 26287 Output IDAT size = 26287 bytes (4868 bytes decrease) Output file size = 26365 bytes (4904 bytes = 15.68% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence_files/figure-html/unnamed-chunk-12-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 25820 bytes Input file size = 25934 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21650 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 = 21650 Output IDAT size = 21650 bytes (4170 bytes decrease) Output file size = 21728 bytes (4206 bytes = 16.22% decrease) --- finished re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’ --- re-building ‘a02_Creating_denominator_populations.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-9-1.png 672x480 pixels, 8 bits/pixel, 236 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6463 bytes Input file size = 7261 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5226 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5190 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 = 1 f = 0 IDAT size = 5190 Output IDAT size = 5190 bytes (1273 bytes decrease) Output file size = 5268 bytes (1993 bytes = 27.45% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-10-1.png 672x480 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6802 bytes Input file size = 7657 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5541 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 = 5541 Output IDAT size = 5541 bytes (1261 bytes decrease) Output file size = 5619 bytes (2038 bytes = 26.62% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-11-1.png 672x480 pixels, 8 bits/pixel, 254 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6892 bytes Input file size = 7744 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5599 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 = 5599 Output IDAT size = 5599 bytes (1293 bytes decrease) Output file size = 5677 bytes (2067 bytes = 26.69% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-13-1.png 672x480 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7218 bytes Input file size = 8073 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5890 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 = 5890 Output IDAT size = 5890 bytes (1328 bytes decrease) Output file size = 5968 bytes (2105 bytes = 26.07% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-14-1.png 672x480 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6563 bytes Input file size = 7418 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5333 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 = 5333 Output IDAT size = 5333 bytes (1230 bytes decrease) Output file size = 5411 bytes (2007 bytes = 27.06% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-17-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35692 bytes Input file size = 35818 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27947 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 = 27947 Output IDAT size = 27947 bytes (7745 bytes decrease) Output file size = 28025 bytes (7793 bytes = 21.76% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-18-1.png 672x768 pixels, 3x8 bits/pixel, RGB Input IDAT size = 47934 bytes Input file size = 48072 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37761 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 = 37761 Output IDAT size = 37761 bytes (10173 bytes decrease) Output file size = 37839 bytes (10233 bytes = 21.29% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-19-1.png 672x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 71868 bytes Input file size = 72042 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52951 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 = 52951 Output IDAT size = 52951 bytes (18917 bytes decrease) Output file size = 53029 bytes (19013 bytes = 26.39% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-20-1.png 672x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 38083 bytes Input file size = 38209 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31650 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 = 31650 Output IDAT size = 31650 bytes (6433 bytes decrease) Output file size = 31728 bytes (6481 bytes = 16.96% decrease) --- finished re-building ‘a02_Creating_denominator_populations.Rmd’ --- re-building ‘a03_Creating_target_denominator_populations.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-4-1.png 288x288 pixels, 8 bits/pixel, 244 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3203 bytes Input file size = 4025 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2769 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 = 2769 Output IDAT size = 2769 bytes (434 bytes decrease) Output file size = 2847 bytes (1178 bytes = 29.27% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-6-1.png 288x288 pixels, 8 bits/pixel, 239 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3471 bytes Input file size = 4278 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3027 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 = 3027 Output IDAT size = 3027 bytes (444 bytes decrease) Output file size = 3105 bytes (1173 bytes = 27.42% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-7-1.png 288x288 pixels, 8 bits/pixel, 246 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3037 bytes Input file size = 3865 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2562 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2555 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 = 1 f = 0 IDAT size = 2555 Output IDAT size = 2555 bytes (482 bytes decrease) Output file size = 2633 bytes (1232 bytes = 31.88% decrease) --- finished re-building ‘a03_Creating_target_denominator_populations.Rmd’ --- re-building ‘a04_Calculating_prevalence.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-6-1.png 672x480 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 9180 bytes Input file size = 10047 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7626 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 = 7626 Output IDAT size = 7626 bytes (1554 bytes decrease) Output file size = 7704 bytes (2343 bytes = 23.32% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-7-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 21563 bytes Input file size = 22445 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20002 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 = 20002 Output IDAT size = 20002 bytes (1561 bytes decrease) Output file size = 20080 bytes (2365 bytes = 10.54% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-8-1.png 672x480 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 9773 bytes Input file size = 10640 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7812 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 = 7812 Output IDAT size = 7812 bytes (1961 bytes decrease) Output file size = 7890 bytes (2750 bytes = 25.85% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-9-1.png 672x480 pixels, 8 bits/pixel, 253 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8600 bytes Input file size = 9461 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7051 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 = 7051 Output IDAT size = 7051 bytes (1549 bytes decrease) Output file size = 7129 bytes (2332 bytes = 24.65% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-10-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 21112 bytes Input file size = 21994 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19579 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 = 19579 Output IDAT size = 19579 bytes (1533 bytes decrease) Output file size = 19657 bytes (2337 bytes = 10.63% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-11-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 21112 bytes Input file size = 21994 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19579 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 = 19579 Output IDAT size = 19579 bytes (1533 bytes decrease) Output file size = 19657 bytes (2337 bytes = 10.63% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-12-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15267 bytes Input file size = 16137 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13390 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 = 13390 Output IDAT size = 13390 bytes (1877 bytes decrease) Output file size = 13468 bytes (2669 bytes = 16.54% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-13-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15894 bytes Input file size = 16764 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14157 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 = 14157 Output IDAT size = 14157 bytes (1737 bytes decrease) Output file size = 14235 bytes (2529 bytes = 15.09% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-14-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 28455 bytes Input file size = 29349 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26399 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 = 26399 Output IDAT size = 26399 bytes (2056 bytes decrease) Output file size = 26477 bytes (2872 bytes = 9.79% decrease) --- finished re-building ‘a04_Calculating_prevalence.Rmd’ --- re-building ‘a05_Calculating_incidence.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-7-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8760 bytes Input file size = 9630 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7247 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 = 7247 Output IDAT size = 7247 bytes (1513 bytes decrease) Output file size = 7325 bytes (2305 bytes = 23.94% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-8-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8731 bytes Input file size = 9601 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7238 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 = 7238 Output IDAT size = 7238 bytes (1493 bytes decrease) Output file size = 7316 bytes (2285 bytes = 23.80% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-9-1.png 672x480 pixels, 8 bits/pixel, 254 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8764 bytes Input file size = 9628 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7250 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 = 7250 Output IDAT size = 7250 bytes (1514 bytes decrease) Output file size = 7328 bytes (2300 bytes = 23.89% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-10-1.png 672x480 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8565 bytes Input file size = 9432 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7096 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 = 7096 Output IDAT size = 7096 bytes (1469 bytes decrease) Output file size = 7174 bytes (2258 bytes = 23.94% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-11-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15082 bytes Input file size = 15952 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13092 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 = 13092 Output IDAT size = 13092 bytes (1990 bytes decrease) Output file size = 13170 bytes (2782 bytes = 17.44% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-12-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15219 bytes Input file size = 16089 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13313 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 = 13313 Output IDAT size = 13313 bytes (1906 bytes decrease) Output file size = 13391 bytes (2698 bytes = 16.77% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-12-2.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 27339 bytes Input file size = 28233 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25241 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 = 25241 Output IDAT size = 25241 bytes (2098 bytes decrease) Output file size = 25319 bytes (2914 bytes = 10.32% decrease) Quitting from lines 249-258 [unnamed-chunk-14] (a05_Calculating_incidence.Rmd) Error: processing vignette 'a05_Calculating_incidence.Rmd' failed with diagnostics: ℹ In argument: `min_cell_count = paste0(...)`. Caused by error in `.data$min_cell_count`: ! Column `min_cell_count` not found in `.data`. --- failed re-building ‘a05_Calculating_incidence.Rmd’ --- re-building ‘a06_Plotting_options.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/facetplot-1.png 672x480 pixels, 8 bits/pixel, 254 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8622 bytes Input file size = 9486 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7145 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 = 7145 Output IDAT size = 7145 bytes (1477 bytes decrease) Output file size = 7223 bytes (2263 bytes = 23.86% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/linesplot-1.png 672x480 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 11872 bytes Input file size = 12739 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10222 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 = 10222 Output IDAT size = 10222 bytes (1650 bytes decrease) Output file size = 10300 bytes (2439 bytes = 19.15% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/noconfplot-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 10960 bytes Input file size = 11830 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9324 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 = 9324 Output IDAT size = 9324 bytes (1636 bytes decrease) Output file size = 9402 bytes (2428 bytes = 20.52% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/stackedplot-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 11257 bytes Input file size = 12127 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9844 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 = 9844 Output IDAT size = 9844 bytes (1413 bytes decrease) Output file size = 9922 bytes (2205 bytes = 18.18% decrease) --- finished re-building ‘a06_Plotting_options.Rmd’ SUMMARY: processing the following file failed: ‘a05_Calculating_incidence.Rmd’ Error: Vignette re-building failed. Execution halted Package: IncidencePrevalence Check: tests New result: ERROR Running ‘testthat.R’ [351s/186s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(IncidencePrevalence) > > test_check("IncidencePrevalence") Starting 2 test processes [ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ] ══ Skipped tests (71) ══════════════════════════════════════════════════════════ • On CRAN (71): 'test-benchmarkIncidencePrevalence.R:2:3', 'test-estimatePrevalence.R:67:3', 'test-estimatePrevalence.R:124:3', 'test-estimatePrevalence.R:244:3', 'test-estimatePrevalence.R:380:3', 'test-estimatePrevalence.R:462:3', 'test-estimatePrevalence.R:607:3', 'test-estimatePrevalence.R:658:3', 'test-estimatePrevalence.R:715:3', 'test-estimatePrevalence.R:763:3', 'test-estimatePrevalence.R:787:3', 'test-estimatePrevalence.R:812:3', 'test-estimatePrevalence.R:945:3', 'test-estimatePrevalence.R:987:3', 'test-estimatePrevalence.R:1017:3', 'test-estimatePrevalence.R:1098:3', 'test-estimatePrevalence.R:1150:3', 'test-estimateIncidence.R:91:3', 'test-estimateIncidence.R:201:3', 'test-estimateIncidence.R:273:3', 'test-estimateIncidence.R:374:3', 'test-estimateIncidence.R:479:3', 'test-estimateIncidence.R:576:3', 'test-estimateIncidence.R:744:3', 'test-estimateIncidence.R:853:3', 'test-estimateIncidence.R:1008:3', 'test-estimateIncidence.R:1074:3', 'test-estimateIncidence.R:1130:3', 'test-estimateIncidence.R:1219:3', 'test-estimateIncidence.R:1394:3', 'test-estimateIncidence.R:1512:3', 'test-estimateIncidence.R:1593:3', 'test-estimateIncidence.R:1703:3', 'test-estimateIncidence.R:1809:3', 'test-estimateIncidence.R:1962:3', 'test-estimateIncidence.R:2019:3', 'test-estimateIncidence.R:2209:3', 'test-estimateIncidence.R:2407:3', 'test-estimateIncidence.R:2485:3', 'test-estimateIncidence.R:2899:3', 'test-estimateIncidence.R:2940:3', 'test-estimateIncidence.R:2989:3', 'test-estimateIncidence.R:3047:3', 'test-mockIncidencePrevalenceRef.R:2:3', 'test-mockIncidencePrevalenceRef.R:39:3', 'test-mockIncidencePrevalenceRef.R:67:3', 'test-mockIncidencePrevalenceRef.R:118:3', 'test-mockIncidencePrevalenceRef.R:220:3', 'test-plotting.R:2:3', 'test-plotting.R:105:3', 'test-plotting.R:160:3', 'test-plotting.R:211:3', 'test-generateDenominatorCohortSet.R:138:3', 'test-generateDenominatorCohortSet.R:185:3', 'test-generateDenominatorCohortSet.R:289:3', 'test-generateDenominatorCohortSet.R:325:3', 'test-generateDenominatorCohortSet.R:581:3', 'test-generateDenominatorCohortSet.R:799:3', 'test-generateDenominatorCohortSet.R:842:3', 'test-generateDenominatorCohortSet.R:894:3', 'test-generateDenominatorCohortSet.R:978:3', 'test-generateDenominatorCohortSet.R:1101:3', 'test-generateDenominatorCohortSet.R:1165:3', 'test-generateDenominatorCohortSet.R:1218:3', 'test-generateDenominatorCohortSet.R:1276:3', 'test-generateDenominatorCohortSet.R:1352:3', 'test-generateDenominatorCohortSet.R:1473:3', 'test-generateDenominatorCohortSet.R:1572:3', 'test-generateDenominatorCohortSet.R:1623:3', 'test-generateDenominatorCohortSet.R:1686:3', 'test-generateDenominatorCohortSet.R:1905:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-benchmarkIncidencePrevalence.R:55:3'): check tables cleaned up ── Error in `omopgenerics::newSummarisedResult(x = prs, settings = dplyr::mutate(dplyr::select(analysisSettings, !c("denominator_cohort_name", "outcome_cohort_name")), dplyr::across(-"result_id", as.character)))`: Each `result_id` must be unique and contain a unique set of settings. Backtrace: ▆ 1. └─IncidencePrevalence::benchmarkIncidencePrevalence(cdm) at test-benchmarkIncidencePrevalence.R:55:3 2. └─IncidencePrevalence::estimatePointPrevalence(...) 3. └─IncidencePrevalence:::estimatePrevalence(...) 4. └─omopgenerics::newSummarisedResult(...) 5. └─omopgenerics:::validateSummarisedResult(x) 6. └─omopgenerics:::validateResultSettings(attr(x, "settings"), call = call) 7. └─cli::cli_abort(...) 8. └─rlang::abort(...) ── Failure ('test-estimatePrevalence.R:1202:3'): mock db: prevalence using strata vars ── visOmopResults::filterSettings(prev_orig, result_type == "prevalence") (`actual`) not equal to ... %>% ... (`expected`). attr(actual, 'settings') vs attr(expected, 'settings') strata - attr(actual, 'settings')[1, ] + attr(expected, 'settings')[1, ] my_strata `attr(actual, 'settings')$strata`: "" `attr(expected, 'settings')$strata`: "my_strata" ── Failure ('test-estimateIncidence.R:3154:3'): mock db: incidence using strata vars ── visOmopResults::filterSettings(inc_orig, result_type == "incidence") (`actual`) not identical to ... %>% ... (`expected`). attr(actual, 'settings') vs attr(expected, 'settings') strata - attr(actual, 'settings')[1, ] + attr(expected, 'settings')[1, ] my_strata `attr(actual, 'settings')$strata`: "" `attr(expected, 'settings')$strata`: "my_strata" ── Error ('test-tables.R:13:3'): test tables ─────────────────────────────────── Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' Backtrace: ▆ 1. └─IncidencePrevalence::tablePrevalence(prev_period, type = "gt") at test-tables.R:13:3 2. └─IncidencePrevalence:::tableInternal(...) 3. └─IncidencePrevalence:::defaultTableIncidencePrevalence(...) ── Failure ('test-tables.R:73:3'): test importing results ────────────────────── Expected `tablePrevalence(prev_period_imported, type = "gt")` to run without any errors. i Actually got a with text: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' ── Failure ('test-tables.R:91:3'): test importing results ────────────────────── Expected `tableIncidence(inc_imported, type = "tibble")` to run without any errors. i Actually got a with text: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' ── Failure ('test-tables.R:98:3'): test importing results ────────────────────── Expected `tableIncidence(results_imported)` to run without any errors. i Actually got a with text: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' ── Failure ('test-tables.R:99:3'): test importing results ────────────────────── Expected `tablePrevalence(results_imported)` to run without any errors. i Actually got a with text: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' [ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ] Error: Test failures Execution halted