Last updated on 2024-09-27 01:49:54 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.2 | 7.21 | 646.04 | 653.25 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.3.0 | 5.56 | 952.51 | 958.07 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.3.0 | 1067.77 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.3.0 | 1061.82 | OK | |||
| r-devel-windows-x86_64 | 0.2.2 | 9.00 | 357.00 | 366.00 | ERROR | |
| r-patched-linux-x86_64 | 0.2.2 | 7.44 | 605.16 | 612.60 | ERROR | |
| r-release-linux-x86_64 | 0.2.2 | 5.83 | 623.14 | 628.97 | ERROR | |
| r-release-macos-arm64 | 0.3.0 | 276.00 | NOTE | |||
| r-release-macos-x86_64 | 0.3.0 | 417.00 | NOTE | |||
| r-release-windows-x86_64 | 0.3.0 | 10.00 | 685.00 | 695.00 | NOTE | |
| r-oldrel-macos-arm64 | 0.3.0 | 347.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.3.0 | 509.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 0.2.2 | 12.00 | 498.00 | 510.00 | ERROR |
Version: 0.2.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [516s/296s]
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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.3.0
Check: installed package size
Result: NOTE
installed size is 9.9Mb
sub-directories of 1Mb or more:
doc 9.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.2.2
Check: tests
Result: ERROR
Running 'testthat.R' [224s]
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 39 | WARN 152 | SKIP 51 | PASS 194 ]
══ 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$cohort5, "subject_id") == c("3", "3")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-requireCohortIntersect.R:74:3'): requiring presence in another cohort ──
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-requireCohortIntersect.R:89:3'): requiring presence in another cohort ──
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-requireCohortIntersect.R:92:3'): requiring presence in another cohort ──
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-requireCohortIntersect.R:107:3'): requiring presence in another cohort ──
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-requireCohortIntersect.R:110:3'): requiring presence in another cohort ──
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-requireConceptIntersect.R:38:3'): require flag in concept ────
all(dplyr::pull(cdm$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 39 | WARN 152 | SKIP 51 | PASS 194 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.2.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [484s/277s]
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 158 | 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$cohort4, 1) (`actual`) not equal to dplyr::tibble(...) (`expected`).
`attr(actual, 'row.names')`: 1
`attr(expected, 'row.names')`: 1 2 3 4 5
actual vs expected
subject_id cohort_start_date cohort_end_date
- actual[1, ] 2 2002-09-08 2002-09-08
+ expected[1, ] 1 2000-07-01 2000-07-01
+ expected[2, ] 1 2000-12-11 2000-12-11
+ expected[3, ] 2 2002-09-08 2002-09-08
+ expected[4, ] 3 2015-02-19 2015-02-19
+ expected[5, ] 3 2015-02-20 2015-02-20
`actual$subject_id`: 2
`expected$subject_id`: 1 1 2 3 3
actual$cohort_start_date | expected$cohort_start_date
[1] "2002-09-08" - "2000-07-01" [1]
- "2000-12-11" [2]
- "2002-09-08" [3]
- "2015-02-19" [4]
- "2015-02-20" [5]
actual$cohort_end_date | expected$cohort_end_date
[1] "2002-09-08" - "2000-07-01" [1]
- "2000-12-11" [2]
- "2002-09-08" [3]
- "2015-02-19" [4]
- "2015-02-20" [5]
── Failure ('test-measurementCohort.R:106:3'): mearurementCohorts works ────────
collectCohort(cdm$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$cohort7, 2) (`actual`) not equal to dplyr::tibble(...) (`expected`).
`attr(actual, 'row.names')`: 1
`attr(expected, 'row.names')`: 1 2 3 4
actual vs expected
subject_id cohort_start_date cohort_end_date
- actual[1, ] 2 2002-09-08 2002-09-08
+ expected[1, ] 1 2000-12-11 2000-12-11
+ expected[2, ] 2 2002-09-08 2002-09-08
+ expected[3, ] 3 2015-02-19 2015-02-19
+ expected[4, ] 3 2015-02-20 2015-02-20
`actual$subject_id`: 2
`expected$subject_id`: 1 2 3 3
actual$cohort_start_date | expected$cohort_start_date
[1] "2002-09-08" - "2000-12-11" [1]
- "2002-09-08" [2]
- "2015-02-19" [3]
- "2015-02-20" [4]
`actual$cohort_end_date`: "2002-09-08"
`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 158 | SKIP 51 | PASS 192 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.2.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [499s/290s]
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 39 | WARN 146 | SKIP 51 | PASS 194 ]
══ 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')`: 1
`attr(expected, 'row.names')`: 1 2
actual vs expected
subject_id cohort_start_date cohort_end_date
actual[1, ] 1 2000-07-01 2000-07-01
+ expected[2, ] 3 2015-02-19 2015-02-19
`actual$subject_id`: 1
`expected$subject_id`: 1 3
`actual$cohort_start_date`: "2000-07-01"
`expected$cohort_start_date`: "2000-07-01" "2015-02-19"
`actual$cohort_end_date`: "2000-07-01"
`expected$cohort_end_date`: "2000-07-01" "2015-02-19"
── Failure ('test-measurementCohort.R:69:3'): mearurementCohorts works ─────────
collectCohort(cdm$cohort3, 1) (`actual`) not equal to dplyr::tibble(...) (`expected`).
`attr(actual, 'row.names')`: 1
`attr(expected, 'row.names')`: 1 2
actual vs expected
subject_id cohort_start_date cohort_end_date
actual[1, ] 1 2000-07-01 2000-07-01
+ expected[2, ] 3 2015-02-19 2015-02-19
`actual$subject_id`: 1
`expected$subject_id`: 1 3
`actual$cohort_start_date`: "2000-07-01"
`expected$cohort_start_date`: "2000-07-01" "2015-02-19"
`actual$cohort_end_date`: "2000-07-01"
`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')`: 1 2
`attr(expected, 'row.names')`: 1 2 3 4 5
actual vs expected
subject_id cohort_start_date cohort_end_date
actual[1, ] 1 2000-07-01 2000-07-01
actual[2, ] 1 2000-12-11 2000-12-11
+ expected[3, ] 2 2002-09-08 2002-09-08
+ expected[4, ] 3 2015-02-19 2015-02-19
+ expected[5, ] 3 2015-02-20 2015-02-20
`actual$subject_id`: 1 1
`expected$subject_id`: 1 1 2 3 3
actual$cohort_start_date | expected$cohort_start_date
[1] "2000-07-01" | "2000-07-01" [1]
[2] "2000-12-11" | "2000-12-11" [2]
- "2002-09-08" [3]
- "2015-02-19" [4]
- "2015-02-20" [5]
actual$cohort_end_date | expected$cohort_end_date
[1] "2000-07-01" | "2000-07-01" [1]
[2] "2000-12-11" | "2000-12-11" [2]
- "2002-09-08" [3]
- "2015-02-19" [4]
- "2015-02-20" [5]
── 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$cohort_end_date`: "2015-02-19" "2015-02-20"
── Failure ('test-measurementCohort.R:150:3'): mearurementCohorts works ────────
collectCohort(cdm$cohort7, 2) (`actual`) not equal to dplyr::tibble(...) (`expected`).
`attr(actual, 'row.names')`: 1
`attr(expected, 'row.names')`: 1 2 3 4
actual vs expected
subject_id cohort_start_date cohort_end_date
actual[1, ] 1 2000-12-11 2000-12-11
+ expected[2, ] 2 2002-09-08 2002-09-08
+ expected[3, ] 3 2015-02-19 2015-02-19
+ expected[4, ] 3 2015-02-20 2015-02-20
`actual$subject_id`: 1
`expected$subject_id`: 1 2 3 3
actual$cohort_start_date | expected$cohort_start_date
[1] "2000-12-11" | "2000-12-11" [1]
- "2002-09-08" [2]
- "2015-02-19" [3]
- "2015-02-20" [4]
`actual$cohort_end_date`: "2000-12-11"
`expected$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 39 | WARN 146 | SKIP 51 | PASS 194 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.2.2
Check: tests
Result: ERROR
Running 'testthat.R' [324s]
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 39 | WARN 146 | SKIP 51 | PASS 194 ]
══ 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$cohort4, 1) (`actual`) not equal to dplyr::tibble(...) (`expected`).
`attr(actual, 'row.names')`: 1
`attr(expected, 'row.names')`: 1 2 3 4 5
actual vs expected
subject_id cohort_start_date cohort_end_date
- actual[1, ] 2 2002-09-08 2002-09-08
+ expected[1, ] 1 2000-07-01 2000-07-01
+ expected[2, ] 1 2000-12-11 2000-12-11
+ expected[3, ] 2 2002-09-08 2002-09-08
+ expected[4, ] 3 2015-02-19 2015-02-19
+ expected[5, ] 3 2015-02-20 2015-02-20
`actual$subject_id`: 2
`expected$subject_id`: 1 1 2 3 3
actual$cohort_start_date | expected$cohort_start_date
[1] "2002-09-08" - "2000-07-01" [1]
- "2000-12-11" [2]
- "2002-09-08" [3]
- "2015-02-19" [4]
- "2015-02-20" [5]
actual$cohort_end_date | expected$cohort_end_date
[1] "2002-09-08" - "2000-07-01" [1]
- "2000-12-11" [2]
- "2002-09-08" [3]
- "2015-02-19" [4]
- "2015-02-20" [5]
── Failure ('test-measurementCohort.R:106:3'): mearurementCohorts works ────────
collectCohort(cdm$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$cohort7, 2) (`actual`) not equal to dplyr::tibble(...) (`expected`).
`attr(actual, 'row.names')`: 1
`attr(expected, 'row.names')`: 1 2 3 4
actual vs expected
subject_id cohort_start_date cohort_end_date
- actual[1, ] 2 2002-09-08 2002-09-08
+ expected[1, ] 1 2000-12-11 2000-12-11
+ expected[2, ] 2 2002-09-08 2002-09-08
+ expected[3, ] 3 2015-02-19 2015-02-19
+ expected[4, ] 3 2015-02-20 2015-02-20
`actual$subject_id`: 2
`expected$subject_id`: 1 2 3 3
actual$cohort_start_date | expected$cohort_start_date
[1] "2002-09-08" - "2000-12-11" [1]
- "2002-09-08" [2]
- "2015-02-19" [3]
- "2015-02-20" [4]
`actual$cohort_end_date`: "2002-09-08"
`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: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-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 39 | WARN 146 | SKIP 51 | PASS 194 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64