Running ‘testthat.R’ [771s/461s]
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(CohortConstructor)
  > 
  > test_check("CohortConstructor")
  Starting 2 test processes
  [ FAIL 41 | WARN 155 | SKIP 51 | PASS 192 ]
  
  ══ Skipped tests (51) ══════════════════════════════════════════════════════════
  • On CRAN (51): 'test-conceptCohort.R:137:3', 'test-conceptCohort.R:209:3',
    'test-conceptCohort.R:237:3', 'test-conceptCohort.R:284:3',
    'test-conceptCohort.R:430:3', 'test-entryAtColumnDate.R:2:3',
    'test-entryAtColumnDate.R:58:3', 'test-exitAtColumnDate.R:2:3',
    'test-exitAtColumnDate.R:62:3', 'test-exitAtColumnDate.R:119:3',
    'test-collapseCohorts.R:95:3', 'test-intersectCohorts.R:13:3',
    'test-intersectCohorts.R:77:3', 'test-intersectCohorts.R:122:3',
    'test-intersectCohorts.R:221:3', 'test-intersectCohorts.R:332:3',
    'test-intersectCohorts.R:373:3', 'test-exitAtDate.R:36:3',
    'test-measurementCohort.R:209:3', 'test-requireCohortIntersect.R:144:3',
    'test-requireCohortIntersect.R:180:3',
    'test-requireConceptIntersect.R:114:3',
    'test-requireConceptIntersect.R:195:3', 'test-requireDateRange.R:2:3',
    'test-requireDateRange.R:102:3', 'test-requireDeathFlag.R:2:3',
    'test-requireDeathFlag.R:78:3', 'test-requireDemographics.R:2:3',
    'test-requireDemographics.R:130:3', 'test-requireDemographics.R:177:3',
    'test-requireDemographics.R:216:3', 'test-requireDemographics.R:241:3',
    'test-requireDemographics.R:265:3', 'test-requireDemographics.R:414:3',
    'test-requireDemographics.R:463:3', 'test-requireDemographics.R:495:3',
    'test-requireIsFirstEntry.R:24:3', 'test-requireIsFirstEntry.R:64:3',
    'test-requireIsFirstEntry.R:88:3', 'test-requireTableIntersect.R:2:3',
    'test-requireTableIntersect.R:102:3', 'test-requireTableIntersect.R:183:3',
    'test-subsetCohorts.R:49:3', 'test-subsetCohorts.R:98:3',
    'test-subsetCohorts.R:117:3', 'test-trimDemographics.R:2:3',
    'test-trimDemographics.R:328:3', 'test-unionCohorts.R:143:3',
    'test-unionCohorts.R:198:3', 'test-yearCohorts.R:2:3',
    'test-yearCohorts.R:122:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-exitAtDate.R:9:3'): exit at observation end ──────────────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-exitAtDate.R:11:3'): exit at observation end ─────────────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-exitAtDate.R:13:3'): exit at observation end ─────────────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-exitAtDate.R:17:3'): exit at observation end ─────────────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-exitAtDate.R:19:3'): exit at observation end ─────────────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-exitAtDate.R:21:3'): exit at observation end ─────────────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-measurementCohort.R:42:3'): mearurementCohorts works ─────────
  collectCohort(cdm$cohort, 1) (`actual`) not equal to dplyr::tibble(...) (`expected`).
  
    `attr(actual, 'row.names')`:    
  `attr(expected, 'row.names')`: 1 2
  
    `actual$subject_id`:    
  `expected$subject_id`: 1 3
  
  `actual$cohort_start_date`:                            
  `expected$cohort_start_date`: "2000-07-01" "2015-02-19"
  
  `actual$cohort_end_date`:                            
  `expected$cohort_end_date`: "2000-07-01" "2015-02-19"
  ── Failure ('test-measurementCohort.R:69:3'): mearurementCohorts works ─────────
  collectCohort(cdm$cohort3, 1) (`actual`) not equal to dplyr::tibble(...) (`expected`).
  
    `attr(actual, 'row.names')`:    
  `attr(expected, 'row.names')`: 1 2
  
    `actual$subject_id`:    
  `expected$subject_id`: 1 3
  
  `actual$cohort_start_date`:                            
  `expected$cohort_start_date`: "2000-07-01" "2015-02-19"
  
  `actual$cohort_end_date`:                            
  `expected$cohort_end_date`: "2000-07-01" "2015-02-19"
  ── Failure ('test-measurementCohort.R:87:3'): mearurementCohorts works ─────────
  collectCohort(cdm$cohort4, 1) (`actual`) not equal to dplyr::tibble(...) (`expected`).
  
    `attr(actual, 'row.names')`:          
  `attr(expected, 'row.names')`: 1 2 3 4 5
  
    `actual$subject_id`:          
  `expected$subject_id`: 1 1 2 3 3
  
   actual$cohort_start_date | expected$cohort_start_date    
                            - "2000-07-01"               [1]
                            - "2000-12-11"               [2]
                            - "2002-09-08"               [3]
                            - "2015-02-19"               [4]
                            - "2015-02-20"               [5]
  
   actual$cohort_end_date | expected$cohort_end_date    
                          - "2000-07-01"             [1]
                          - "2000-12-11"             [2]
                          - "2002-09-08"             [3]
                          - "2015-02-19"             [4]
                          - "2015-02-20"             [5]
  ── Failure ('test-measurementCohort.R:106:3'): mearurementCohorts works ────────
  collectCohort(cdm$cohort5, 1) (`actual`) not equal to dplyr::tibble(...) (`expected`).
  
    `attr(actual, 'row.names')`:  
  `attr(expected, 'row.names')`: 1
  
    `actual$subject_id`:  
  `expected$subject_id`: 1
  
  `actual$cohort_start_date`:               
  `expected$cohort_start_date`: "2000-07-01"
  
  `actual$cohort_end_date`:               
  `expected$cohort_end_date`: "2000-07-01"
  ── Failure ('test-measurementCohort.R:125:3'): mearurementCohorts works ────────
  collectCohort(cdm$cohort6, 1) (`actual`) not equal to dplyr::tibble(...) (`expected`).
  
    `attr(actual, 'row.names')`:    
  `attr(expected, 'row.names')`: 1 2
  
    `actual$subject_id`:    
  `expected$subject_id`: 3 3
  
  `actual$cohort_start_date`:                            
  `expected$cohort_start_date`: "2015-02-19" "2015-02-20"
  
  `actual$cohort_end_date`:                            
  `expected$cohort_end_date`: "2015-02-19" "2015-02-20"
  ── Failure ('test-measurementCohort.R:143:3'): mearurementCohorts works ────────
  collectCohort(cdm$cohort7, 1) (`actual`) not equal to dplyr::tibble(...) (`expected`).
  
    `attr(actual, 'row.names')`:  
  `attr(expected, 'row.names')`: 1
  
    `actual$subject_id`:  
  `expected$subject_id`: 1
  
  `actual$cohort_start_date`:               
  `expected$cohort_start_date`: "2000-07-01"
  
  `actual$cohort_end_date`:               
  `expected$cohort_end_date`: "2000-07-01"
  ── Failure ('test-measurementCohort.R:150:3'): mearurementCohorts works ────────
  collectCohort(cdm$cohort7, 2) (`actual`) not equal to dplyr::tibble(...) (`expected`).
  
    `attr(actual, 'row.names')`:        
  `attr(expected, 'row.names')`: 1 2 3 4
  
    `actual$subject_id`:        
  `expected$subject_id`: 1 2 3 3
  
   actual$cohort_start_date | expected$cohort_start_date    
                            - "2000-12-11"               [1]
                            - "2002-09-08"               [2]
                            - "2015-02-19"               [3]
                            - "2015-02-20"               [4]
  
  `actual$cohort_end_date`:                                                      
  `expected$cohort_end_date`: "2000-12-11" "2002-09-08" "2015-02-19" "2015-02-20"
  ── Failure ('test-requireCohortIntersect.R:72:3'): requiring presence in another cohort ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireCohortIntersect.R:73:3'): requiring presence in another cohort ──
  all(dplyr::pull(cdm$cohort5, "subject_id") == c("3", "3")) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireCohortIntersect.R:74:3'): requiring presence in another cohort ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireCohortIntersect.R:89:3'): requiring presence in another cohort ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireCohortIntersect.R:92:3'): requiring presence in another cohort ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireCohortIntersect.R:93:3'): requiring presence in another cohort ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireCohortIntersect.R:107:3'): requiring presence in another cohort ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireCohortIntersect.R:110:3'): requiring presence in another cohort ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireCohortIntersect.R:111:3'): requiring presence in another cohort ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireConceptIntersect.R:38:3'): require flag in concept ────
  all(dplyr::pull(cdm$cohort3, "subject_id") == rep(1, 5)) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireConceptIntersect.R:40:3'): require flag in concept ────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireConceptIntersect.R:54:3'): require flag in concept ────
  all(dplyr::pull(cdm$cohort4, "subject_id") == c(rep(1, 5), 3)) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireConceptIntersect.R:56:3'): require flag in concept ────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireConceptIntersect.R:68:3'): require flag in concept ────
  length(dplyr::pull(cdm$cohort5, "subject_id")) == 0 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireIsFirstEntry.R:8:3'): test restrict to first entry works ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireIsFirstEntry.R:14:3'): test restrict to first entry works ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-requireIsFirstEntry.R:18:3'): test restrict to first entry works ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-sampleCohorts.R:41:3'): sampleCohort subsetting multiple cohorts ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-sampleCohorts.R:53:3'): sampleCohort subsetting multiple cohorts ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-unionCohorts.R:9:3'): unionCohorts works ─────────────────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-unionCohorts.R:13:3'): unionCohorts works ────────────────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-unionCohorts.R:17:3'): unionCohorts works ────────────────────
  all(cdm$cohort2 %>% dplyr::pull("subject_id") %>% sort() == 1:4) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-unionCohorts.R:20:3'): unionCohorts works ────────────────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-unionCohorts.R:34:3'): unionCohorts works ────────────────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-unionCohorts.R:38:3'): unionCohorts works ────────────────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-unionCohorts.R:42:3'): unionCohorts works ────────────────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-unionCohorts.R:45:3'): unionCohorts works ────────────────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Error ('test-unionCohorts.R:84:3'): gap and name works ──────────────────────
  Error in `validateGeneratedCohortSet(cohort, soft = .softValidation)`: ! 3 observations outside observation period.
  Backtrace:
      ▆
   1. └─omopgenerics::newCohortTable(cdm$cohort1) at test-unionCohorts.R:84:3
   2.   └─omopgenerics:::validateGeneratedCohortSet(cohort, soft = .softValidation)
   3.     └─omopgenerics::validateCohortArgument(...)
   4.       └─omopgenerics:::checkObservationPeriod(...)
   5.         └─cli::cli_abort(message = mes, call = call)
   6.           └─rlang::abort(...)
  
  [ FAIL 41 | WARN 155 | SKIP 51 | PASS 192 ]
  Error: Test failures
  Execution halted