Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [251s/150s]
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(PatientProfiles)
  > 
  > test_check("PatientProfiles")
  Starting 2 test processes.
  > test-addConceptIntersect.R: ! The following columns will be overwritten:
  > test-addConceptIntersect.R: * intersect
  > test-addConceptIntersect.R: ! The following columns will be overwritten:
  > test-addConceptIntersect.R: * intersect
  > test-addConceptIntersect.R: ! The following columns will be overwritten:
  > test-addConceptIntersect.R: * intersect
  > test-addConceptIntersect.R: ! The following columns will be overwritten:
  > test-addConceptIntersect.R: * intersect
  > test-addConceptIntersect.R: ! The following columns will be overwritten:
  > test-addConceptIntersect.R: * intersect
  > test-addConceptIntersect.R: ! The following columns will be overwritten:
  > test-addConceptIntersect.R: * intersect
  > test-addConceptIntersect.R: ! The following columns will be overwritten:
  > test-addConceptIntersect.R: * intersect
  > test-summariseResult.R: i The following estimates will be computed:
  > test-summariseResult.R: * s: count, percentage
  > test-summariseResult.R: * v_1: min, q25, median, q75, max
  > test-summariseResult.R: * v_2: count, percentage
  > test-summariseResult.R: * v_3: min, q25, median, q75, max, count, percentage
  > test-summariseResult.R: * v_4: min, q25, median, q75, max
  > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:05:52.697463
  > test-summariseResult.R: v Summary finished, at 2025-12-06 13:05:52.943347
  > test-summariseResult.R: i The following estimates will be computed:
  > test-summariseResult.R: * s: count, percentage
  > test-summariseResult.R: * v_1: min, q25, median, q75, max
  > test-summariseResult.R: * v_2: count, percentage
  > test-summariseResult.R: * 
  > test-summariseResult.R: v_3: min, q25, median, q75, max, count, percentage
  > test-summariseResult.R: * v_4: min, q25, median, q75, max
  > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:05:53.738188
  > test-summariseResult.R: v Summary finished, at 2025-12-06 13:05:54.216968
  > test-summariseResult.R: i The following estimates will be computed:
  > test-summariseResult.R: * s: count, percentage
  > test-summariseResult.R: * v_1: min, q25, median, q75, max
  > test-summariseResult.R: * v_2: count, percentage
  > test-summariseResult.R: * v_3: min, q25, median, q75, max, count, percentage
  > test-summariseResult.R: * v_4: min, q25, median, q75, max
  > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:05:54.9844
  > test-summariseResult.R: v Summary finished, at 2025-12-06 13:05:55.497245
  > test-summariseResult.R: ! names of strata will be ignored
  > test-summariseResult.R: i The following estimates will be computed:
  > test-summariseResult.R: * s: count, percentage
  > test-summariseResult.R: * v_1: min, q25, median, q75, max
  > test-summariseResult.R: * v_2: count, percentage
  > test-summariseResult.R: * v_3: min, q25, median, q75, max, count, percentage
  > test-summariseResult.R: * v_4: min, q25, median, q75, max
  > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:05:56.348228
  > test-summariseResult.R: v Summary finished, at 2025-12-06 13:05:57.044397
  > test-summariseResult.R: i The following estimates will be computed:
  > test-summariseResult.R: * cohort_start_date: min, q25, median, q75, max
  > test-summariseResult.R: * cohort_end_date: min, q25, median, q75, max
  > test-summariseResult.R: * acetaminophen_m365_to_0: min, q25, median, q75, max, count, percentage
  > test-summariseResult.R: * ibuprophen_m365_to_0: min, q25, median, q75, max, count, percentage
  > test-summariseResult.R: * naloxone_m365_to_0: min, q25, median, q75, max, count, percentage
  > test-summariseResult.R: * headache_minf_to_0: min, q25, median, q75, max, count, percentage
  > test-summariseResult.R: * covid_minf_to_0: min, q25, median, q75, max, count, percentage
  > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:05:58.171679
  > test-summariseResult.R: v Summary finished, at 2025-12-06 13:05:58.376344
  > test-summariseResult.R: i The following estimates will be computed:
  > test-summariseResult.R: * condition_start_date: min, q25, median, q75, max
  > test-summariseResult.R: * condition_end_date: min, q25, median, q75, max
  > test-summariseResult.R: * age: min, q25, median, q75, max
  > test-summariseResult.R: * age_group: count, percentage
  > test-summariseResult.R: * sex: count, percentage
  > test-summariseResult.R: * prior_observation: min, q25, median, q75, max
  > test-summariseResult.R: * future_observation: min, q25, median, q75, max
  > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:08.173465
  > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:08.588949
  > test-summariseResult.R: i The following estimates will be computed:
  > test-summariseResult.R: * condition_start_date: min, q25, median, q75, max
  > test-summariseResult.R: * condition_end_date: min, q25, median, q75, max
  > test-summariseResult.R: * age: min, q25, median, q75, max
  > test-summariseResult.R: * age_group: count, percentage
  > test-summariseResult.R: * sex: count, percentage
  > test-summariseResult.R: * prior_observation: min, q25, median, q75, max
  > test-summariseResult.R: * future_observation: min, q25, median, q75, max
  > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:09.917808
  > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:10.360952
  > test-summariseResult.R: i The following estimates will be computed:
  > test-summariseResult.R: * condition_start_date: min, q25, median, q75, max
  > test-summariseResult.R: * condition_end_date: min, q25, median, q75, max
  > test-summariseResult.R: * age: min, q25, median, q75, max
  > test-summariseResult.R: * age_group: count, percentage
  > test-summariseResult.R: * sex: count, percentage
  > test-summariseResult.R: * prior_observation: min, q25, median, q75, max
  > test-summariseResult.R: * future_observation: min, q25, median, q75, max
  > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:11.770981
  > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:12.012252
  > test-summariseResult.R: i The following estimates will be computed:
  > test-summariseResult.R: * condition_start_date: min, q25, median, q75, max
  > test-summariseResult.R: * condition_end_date: min, q25, median, q75, max
  > test-summariseResult.R: * sex: count, percentage
  > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:12.552131
  > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:12.758888
  > test-summariseResult.R: i The following estimates will be computed:
  > test-summariseResult.R: * condition_start_date: min, q25, median, q75, max
  > test-summariseResult.R: * condition_end_date: min, q25, median, q75, max
  > test-summariseResult.R: * age: min, q25, median, q75, max
  > test-summariseResult.R: * age_group: count, percentage
  > test-summariseResult.R: * sex: count, percentage
  > test-summariseResult.R: * prior_observation: min, q25, median, q75, max
  > test-summariseResult.R: * future_observation: min, q25, median, q75, max
  > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:22.508871
  > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:22.958998
  > test-summariseResult.R: i The following estimates will be computed:
  > test-summariseResult.R: * condition_start_date: min, q25, median, q75, max
  > test-summariseResult.R: * condition_end_date: min, q25, m
  > test-summariseResult.R: edian, q75, max
  > test-summariseResult.R: * age: min, q25, median, q75, max
  > test-summariseResult.R: * age_group: count, percentage
  > test-summariseResult.R: * sex: count, percentage
  > test-summariseResult.R: * prior_observation: min, q25, median, q75, max
  > test-summariseResult.R: * future_observation: min, q25, median, q75, max
  > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:24.515288
  > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:24.948116
  > test-summariseResult.R: i The following estimates will be computed:
  > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:25.579398
  > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:25.689426
  > test-summariseResult.R: i The following estimates will be computed:
  > test-summariseResult.R: * group: count
  > test-summariseResult.R: * age1: density, mean
  > test-summariseResult.R: * age2: density, mean
  > test-summariseResult.R: * asthma: density, mean, count
  > test-summariseResult.R: * birth: density, mean
  > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:31.787613
  > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:32.040127
  > test-summariseResult.R: i The following estimates will be computed:
  > test-summariseResult.R: * group: count
  > test-summariseResult.R: * age1: density, mean
  > test-summariseResult.R: * age2: density, mean
  > test-summariseResult.R: * asthma: density, mean, count
  > test-summariseResult.R: * birth: density, mean
  > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:32.853218
  > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:33.408595
  > test-summariseResult.R: i The following estimates will be computed:
  > test-summariseResult.R: * age1: density
  > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:34.173415
  > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:34.321866
  Saving _problems/test-summariseResult-59.R
  Saving _problems/test-summariseResult-60.R
  Saving _problems/test-summariseResult-827.R
  Saving _problems/test-summariseResult-831.R
  [ FAIL 4 | WARN 53 | SKIP 108 | PASS 176 ]
  
  ══ Skipped tests (108) ═════════════════════════════════════════════════════════
  • On CRAN (108): 'test-addAttributes.R:2:3', 'test-addCategories.R:2:3',
    'test-addCategories.R:70:3', 'test-addCategories.R:109:3',
    'test-addCategories.R:157:3', 'test-addConceptIntersect.R:2:3',
    'test-addConceptIntersect.R:100:3', 'test-addConceptIntersect.R:152:3',
    'test-addConceptIntersect.R:195:3', 'test-addConceptIntersect.R:228:3',
    'test-addConceptIntersect.R:261:3', 'test-addCohortIntersect.R:272:3',
    'test-addCohortIntersect.R:347:3', 'test-addCohortIntersect.R:393:3',
    'test-addCohortIntersect.R:502:3', 'test-addCohortIntersect.R:592:3',
    'test-addCohortIntersect.R:650:3', 'test-addCohortIntersect.R:722:3',
    'test-addCohortIntersect.R:744:3', 'test-addCohortIntersect.R:830:3',
    'test-addCohortIntersect.R:884:3', 'test-addCohortIntersect.R:942:3',
    'test-addDeath.R:101:3', 'test-addDeath.R:143:3', 'test-addDeath.R:241:3',
    'test-addDeath.R:281:3', 'test-addFutureObservation.R:2:3',
    'test-addFutureObservation.R:14:3', 'test-addFutureObservation.R:30:3',
    'test-addFutureObservation.R:90:3', 'test-addFutureObservation.R:150:3',
    'test-addFutureObservation.R:212:3', 'test-addFutureObservation.R:256:3',
    'test-addInObservation.R:2:3', 'test-addInObservation.R:18:3',
    'test-addInObservation.R:49:3', 'test-addInObservation.R:173:3',
    'test-addIntersect.R:2:3', 'test-addIntersect.R:37:3',
    'test-addIntersect.R:226:3', 'test-addIntersect.R:277:3',
    'test-addIntersect.R:398:3', 'test-addIntersect.R:502:3',
    'test-addIntersect.R:558:3', 'test-addIntersect.R:626:3',
    'test-addIntersect.R:775:3', 'test-addIntersect.R:855:3',
    'test-addIntersect.R:872:3', 'test-addIntersect.R:942:3',
    'test-addIntersect.R:1028:3', 'test-addIntersect.R:1209:3',
    'test-addIntersect.R:1225:3', 'test-addObservationPeriodId.R:2:3',
    'test-addPriorObservation.R:2:3', 'test-addPriorObservation.R:14:3',
    'test-addPriorObservation.R:30:3', 'test-addPriorObservation.R:76:3',
    'test-addPriorObservation.R:121:3', 'test-addPriorObservation.R:184:3',
    'test-addSex.R:2:3', 'test-addSex.R:16:3', 'test-addSex.R:33:3',
    'test-addSex.R:76:3', 'test-addTableIntersect.R:31:3',
    'test-addTableIntersect.R:216:3', 'test-addTableIntersect.R:324:3',
    'test-addTableIntersect.R:460:3', 'test-addTableIntersect.R:591:3',
    'test-benchmarkPatientProfiles.R:2:3', 'test-checks.R:2:3',
    'test-checks.R:100:3', 'test-checks.R:153:3', 'test-checks.R:170:3',
    'test-checks.R:220:3', 'test-checks.R:247:3', 'test-filterCohortId.R:2:3',
    'test-addDemographics.R:2:3', 'test-addDemographics.R:26:3',
    'test-addDemographics.R:353:3', 'test-addDemographics.R:422:3',
    'test-addDemographics.R:697:3', 'test-addDemographics.R:849:3',
    'test-addDemographics.R:870:3', 'test-addDemographics.R:982:3',
    'test-addDemographics.R:1058:3', 'test-addDemographics.R:1172:3',
    'test-addDemographics.R:1238:3', 'test-addDemographics.R:1267:3',
    'test-addDemographics.R:1297:3', 'test-addDemographics.R:1316:3',
    'test-addDemographics.R:1330:3', 'test-addDemographics.R:1351:3',
    'test-addDemographics.R:1381:3', 'test-format.R:2:3', 'test-format.R:89:3',
    'test-format.R:100:3', 'test-format.R:110:3', 'test-format.R:139:3',
    'test-mockPatientProfiles.R:2:3', 'test-name.R:2:3', 'test-utilities.R:2:3',
    'test-summariseResult.R:255:3', 'test-summariseResult.R:300:3',
    'test-summariseResult.R:365:3', 'test-summariseResult.R:409:3',
    'test-summariseResult.R:431:3', 'test-summariseResult.R:508:3',
    'test-summariseResult.R:596:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-summariseResult.R:57:3'): test all functions ─────────────────
  Expected `x2 <- summariseResult(table = x, strata = list(), weights = "w")` not to throw any errors.
  Actually got a <rlib_error_package_not_found> with message:
    The package "Hmisc" is required.
  ── Error ('test-summariseResult.R:60:3'): test all functions ───────────────────
  Error in `eval(code, test_env)`: object 'x2' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_true(nrow(x1) == nrow(x2)) at test-summariseResult.R:60:3
   2. │ └─testthat::quasi_label(enquo(object), label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::nrow(x2)
  ── Failure ('test-summariseResult.R:827:3'): density works correctly ───────────
  Expected `... <- NULL` not to throw any errors.
  Actually got a <rlib_error_package_not_found> with message:
    The package "Hmisc" is required.
  ── Error ('test-summariseResult.R:828:3'): density works correctly ─────────────
  Error in `eval(code, test_env)`: object 'sw' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-summariseResult.R:828:3
   2. │ └─testthat::quasi_label(enquo(expected), expected.label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─dplyr::pull(...)
   5. └─dplyr::filter(...)
  
  [ FAIL 4 | WARN 53 | SKIP 108 | PASS 176 ]
  Error:
  ! Test failures.
  Execution halted