* using log directory 'd:/RCompile/CRANincoming/R-devel/CohortConstructor.Rcheck'
* using R Under development (unstable) (2025-01-15 r87581 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'CohortConstructor/DESCRIPTION' ... OK
* this is package 'CohortConstructor' version '0.3.4'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [14s] NOTE
Maintainer: 'Edward Burn <edward.burn@ndorms.ox.ac.uk>'

Unknown, possibly misspelled, fields in DESCRIPTION:
  'Remotes'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CohortConstructor' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [15s] NOTE
extendOverlap: no visible binding for global variable 'record_id'
extendOverlap: no visible binding for global variable
  'record_id_overlap'
extendOverlap: no visible binding for global variable
  'cohort_start_date'
extendOverlap: no visible binding for global variable
  'cohort_end_date_overlap'
extendOverlap: no visible binding for global variable 'cohort_end_date'
extendOverlap: no visible binding for global variable
  'cohort_start_date_overlap'
Undefined global functions or variables:
  cohort_end_date cohort_end_date_overlap cohort_start_date
  cohort_start_date_overlap record_id record_id_overlap
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [91s] ERROR
  Running 'testthat.R' [91s]
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 4 | WARN 9 | SKIP 121 | PASS 50 ]
  
  ══ Skipped tests (121) ═════════════════════════════════════════════════════════
  • On CRAN (121): 'test-addIndex.R:2:3', 'test-addIndex.R:24:3',
    'test-collapseCohorts.R:2:3', 'test-collapseCohorts.R:108:3',
    'test-collapseCohorts.R:195:3', 'test-collapseCohorts.R:253:3',
    'test-collapseCohorts.R:317:3', 'test-demographicsCohort.R:2:3',
    'test-demographicsCohort.R:42:3', 'test-demographicsCohort.R:78:3',
    'test-demographicsCohort.R:108:3', 'test-demographicsCohort.R:144:3',
    'test-demographicsCohort.R:215:3', 'test-entryAtColumnDate.R:2:3',
    'test-entryAtColumnDate.R:64:3', 'test-entryAtColumnDate.R:147:3',
    'test-exitAtColumnDate.R:2:3', 'test-exitAtColumnDate.R:67:3',
    'test-exitAtColumnDate.R:138:3', 'test-exitAtColumnDate.R:215:3',
    'test-exitAtDate.R:118:3', 'test-exitAtDate.R:174:3',
    'test-intersectCohorts.R:2:3', 'test-intersectCohorts.R:50:3',
    'test-intersectCohorts.R:101:3', 'test-intersectCohorts.R:148:3',
    'test-intersectCohorts.R:205:3', 'test-intersectCohorts.R:286:3',
    'test-intersectCohorts.R:337:3', 'test-intersectCohorts.R:394:3',
    'test-intersectCohorts.R:441:3', 'test-intersectCohorts.R:548:3',
    'test-intersectCohorts.R:604:3', 'test-intersectCohorts.R:644:3',
    'test-matchCohorts.R:2:3', 'test-matchCohorts.R:79:3',
    'test-matchCohorts.R:124:3', 'test-matchCohorts.R:184:3',
    'test-matchCohorts.R:284:3', 'test-matchCohorts.R:313:3',
    'test-measurementCohort.R:2:3', 'test-measurementCohort.R:244:3',
    'test-measurementCohort.R:329:3', 'test-measurementCohort.R:385:3',
    'test-padCohortDate.R:2:3', 'test-padCohortDate.R:57:3',
    'test-padCohortDate.R:129:3', 'test-padCohortDate.R:166:3',
    'test-padCohortDate.R:317:3', 'test-padCohortDate.R:354:3',
    'test-requireCohortIntersect.R:2:3', 'test-requireCohortIntersect.R:144:3',
    'test-requireCohortIntersect.R:180:3', 'test-requireCohortIntersect.R:299:3',
    'test-requireConceptIntersect.R:2:3', 'test-requireConceptIntersect.R:123:3',
    'test-requireConceptIntersect.R:204:3',
    'test-requireConceptIntersect.R:311:3', 'test-requireDateRange.R:2:3',
    'test-requireDateRange.R:101:3', 'test-requireDateRange.R:159:3',
    'test-requireDeathFlag.R:2:3', 'test-requireDeathFlag.R:78:3',
    'test-requireDeathFlag.R:123:3', 'test-requireDemographics.R:2:3',
    'test-requireDemographics.R:123:3', 'test-requireDemographics.R:168:3',
    'test-requireDemographics.R:207:3', 'test-requireDemographics.R:232:3',
    'test-requireDemographics.R:256:3', 'test-requireDemographics.R:407:3',
    'test-requireDemographics.R:453:3', 'test-requireDemographics.R:482:3',
    'test-requireDemographics.R:510:3', 'test-requireDemographics.R:531:3',
    'test-requireIsEntry.R:24:3', 'test-requireIsEntry.R:62:3',
    'test-requireIsEntry.R:76:3', 'test-requireIsEntry.R:119:3',
    'test-requireIsEntry.R:218:3', 'test-requireMinCohortCount.R:2:3',
    'test-requireMinCohortCount.R:110:3', 'test-requireTableIntersect.R:2:3',
    'test-requireTableIntersect.R:97:3', 'test-requireTableIntersect.R:176:3',
    'test-requireTableIntersect.R:292:3', 'test-sampleCohorts.R:2:3',
    'test-sampleCohorts.R:32:3', 'test-sampleCohorts.R:62:3',
    'test-sampleCohorts.R:82:3', 'test-sampleCohorts.R:105:3',
    'test-sampleCohorts.R:126:3', 'test-stratifyCohorts.R:2:3',
    'test-stratifyCohorts.R:129:3', 'test-subsetCohorts.R:2:3',
    'test-subsetCohorts.R:47:3', 'test-subsetCohorts.R:94:3',
    'test-subsetCohorts.R:113:3', 'test-trimDemographics.R:2:3',
    'test-trimDemographics.R:324:3', 'test-trimDemographics.R:386:3',
    'test-unionCohorts.R:2:3', 'test-unionCohorts.R:76:3',
    'test-unionCohorts.R:153:3', 'test-unionCohorts.R:206:3',
    'test-unionCohorts.R:283:3', 'test-unionCohorts.R:307:3',
    'test-unionCohorts.R:346:3', 'test-yearCohorts.R:2:3',
    'test-yearCohorts.R:119:3', 'test-yearCohorts.R:190:3',
    'test-conceptCohort.R:2:3', 'test-conceptCohort.R:216:3',
    'test-conceptCohort.R:246:3', 'test-conceptCohort.R:293:3',
    'test-conceptCohort.R:439:3', 'test-conceptCohort.R:485:3',
    'test-conceptCohort.R:557:3', 'test-conceptCohort.R:614:3',
    'test-conceptCohort.R:678:3', 'test-conceptCohort.R:888:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-conceptCohort.R:139:3'): simple example ──────────────────────
  dplyr::pull(dplyr::tally(cohort)) == 2 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-conceptCohort.R:140:3'): simple example ──────────────────────
  cohortCount(cohort)$number_records == 2 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-conceptCohort.R:149:3'): simple example ──────────────────────
  dplyr::as_tibble(attrition(cohort)) (`actual`) not identical to dplyr::tibble(...) (`expected`).
  
  actual vs expected
                  number_records excluded_records
    actual[1, ]                9                0
    actual[2, ]                9                0
  - actual[3, ]                5                4
  + expected[3, ]              4                5
  - actual[4, ]                3                2
  + expected[4, ]              2                2
  
    `actual$number_records`: 9 9 5 3
  `expected$number_records`: 9 9 4 2
  
    `actual$excluded_records`: 0 0 4 2
  `expected$excluded_records`: 0 0 5 2
  ── Failure ('test-conceptCohort.R:172:3'): simple example ──────────────────────
  `cohort` (`actual`) not equal to dplyr::tibble(...) (`expected`).
  
    `attr(actual, 'row.names')`: 1 2 3
  `attr(expected, 'row.names')`: 1 2  
  
  actual vs expected
                  cohort_definition_id subject_id cohort_start_date cohort_end_date
    actual[1, ]                      1          1        2020-01-01      2022-03-11
  - actual[2, ]                      1          1        2024-02-09      2024-05-19
  - actual[3, ]                      1          2        2020-01-11      2024-02-22
  + expected[2, ]                    1          2        2020-01-11      2024-01-01
  
    `actual$cohort_definition_id`: 1 1 1
  `expected$cohort_definition_id`: 1 1  
  
    `actual$subject_id`: 1 1 2
  `expected$subject_id`: 1   2
  
  `actual$cohort_start_date`:   "2020-01-01" "2024-02-09" "2020-01-11"
  `expected$cohort_start_date`: "2020-01-01"              "2020-01-11"
  
  `actual$cohort_end_date`:   "2022-03-11" "2024-05-19" "2024-02-22"
  `expected$cohort_end_date`: "2022-03-11" "2024-01-01"             
  
  [ FAIL 4 | WARN 9 | SKIP 121 | PASS 50 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [393s] OK
* checking PDF version of manual ... [23s] OK
* checking HTML version of manual ... [11s] OK
* DONE
Status: 1 ERROR, 2 NOTEs