R Under development (unstable) (2024-09-23 r87189 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # 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(OmopSketch) > > test_check("OmopSketch") Starting 2 test processes [ FAIL 10 | WARN 0 | SKIP 20 | PASS 35 ] ══ Skipped tests (20) ══════════════════════════════════════════════════════════ • On CRAN (20): 'test-mockOmopSketch.R:2:3', 'test-plotInObservation.R:2:3', 'test-summariseClinicalRecords.R:2:3', 'test-summariseClinicalRecords.R:81:3', 'test-summariseClinicalRecords.R:214:3', 'test-summariseInObservation.R:2:3', 'test-summariseInObservation.R:96:3', 'test-summariseInObservation.R:148:3', 'test-summariseInObservation.R:184:3', 'test-summariseOmopSnapshot.R:2:3', 'test-summariseOmopSnapshot.R:10:3', 'test-summariseConceptCounts.R:2:3', 'test-summariseConceptCounts.R:428:3', 'test-summariseRecordCount.R:2:3', 'test-summariseRecordCount.R:92:3', 'test-summariseRecordCount.R:112:3', 'test-summariseRecordCount.R:189:3', 'test-summarisePopulationCharacteristics.R:2:3', 'test-summarisePopulationCharacteristics.R:151:3', 'test-summarisePopulationCharacteristics.R:167:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-summariseObservationPeriod.R:41:3'): check summariseObservationPeriod works ── Expected `resAll <- summariseObservationPeriod(cdm$observation_period)` to run without any errors. i Actually got a with text: unused argument (minFutureObservation = NULL) ── Failure ('test-summariseObservationPeriod.R:42:3'): check summariseObservationPeriod works ── Expected `... <- NULL` to run without any errors. i Actually got a with text: unused argument (minFutureObservation = NULL) ── Failure ('test-summariseObservationPeriod.R:44:3'): check summariseObservationPeriod works ── Expected `... <- NULL` to run without any errors. i Actually got a with text: unused argument (minFutureObservation = NULL) ── Error ('test-summariseObservationPeriod.R:4:5'): check summariseObservationPeriod works ── Error in `eval(code, test_env)`: object 'resAllD' not found Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-summariseObservationPeriod.R:49:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─OmopSketch (local) removeSettings(...) 5. ├─dplyr::mutate(...) at test-summariseObservationPeriod.R:4:5 6. └─dplyr::filter(resAllD, !is.na(variable_level)) ── Error ('test-summariseObservationPeriod.R:276:3'): check it works with mockOmopSketch ── Error in `CohortConstructor::demographicsCohort(cdm, name = paste0(tablePrefix, "demographics_table"), sex = NULL, ageRange = ageGroup, minPriorObservation = NULL, minFutureObservation = NULL)`: unused argument (minFutureObservation = NULL) Backtrace: ▆ 1. ├─OmopSketch::summariseObservationPeriod(cdm$observation_period) at test-summariseObservationPeriod.R:276:3 2. │ ├─dplyr::collect(...) 3. │ ├─dplyr::select(...) 4. │ ├─dplyr::ungroup(...) 5. │ ├─... %>% ... 6. │ ├─dplyr::mutate(...) 7. │ ├─dplyr::arrange(...) 8. │ ├─dplyr::group_by(...) 9. │ ├─dplyr::select(...) 10. │ ├─OmopSketch:::filterPersonId(...) 11. │ │ └─omopgenerics::cdmReference(omopTable) 12. │ │ └─omopgenerics::assertClass(table, "cdm_table") 13. │ │ ├─omopgenerics:::checkClass(...) 14. │ │ ├─omopgenerics:::checkLength(...) 15. │ │ ├─omopgenerics:::checkNull(createCheckObject(x), null) 16. │ │ └─omopgenerics:::createCheckObject(x) 17. │ └─OmopSketch:::addStrataToPeopleInObservation(...) 18. │ ├─base::suppressWarnings(...) 19. │ │ └─base::withCallingHandlers(...) 20. │ └─base::suppressMessages(...) 21. │ └─base::withCallingHandlers(...) 22. └─dplyr::mutate(...) ── Failure ('test-summariseObservationPeriod.R:372:3'): check summariseObservationPeriod strata works ── Expected `... <- NULL` to run without any errors. i Actually got a with text: unused argument (minFutureObservation = NULL) ── Failure ('test-summariseObservationPeriod.R:374:3'): check summariseObservationPeriod strata works ── Expected `... <- NULL` to run without any errors. i Actually got a with text: unused argument (minFutureObservation = NULL) ── Error ('test-summariseObservationPeriod.R:379:3'): check summariseObservationPeriod strata works ── Error in `eval(code, test_env)`: object 'resStrata' not found Backtrace: ▆ 1. ├─dplyr::inner_join(...) at test-summariseObservationPeriod.R:379:3 2. ├─dplyr::rename(...) 3. └─dplyr::filter(...) ── Failure ('test-summarisePopulationCharacteristics.R:127:3'): summarisePopulationCharacteristics() works ── `... <- NULL` did not throw the expected warning. ── Failure ('test-summarisePopulationCharacteristics.R:185:3'): summarisePopulationCharacteristics() works with mockOmopSKetch ── `summarisedPopulation <- summarisePopulationCharacteristics(cdm = cdm)` did not throw the expected warning. [ FAIL 10 | WARN 0 | SKIP 20 | PASS 35 ] Error: Test failures Execution halted