Package check result: OK

Changes to worse in reverse depends:

Package: CohortCharacteristics
Check: examples
New result: ERROR
  Running examples in ‘CohortCharacteristics-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: availablePlotColumns
  > ### Title: Available columns to use in 'facet' and 'colour' arguments in
  > ###   plot functions.
  > ### Aliases: availablePlotColumns
  > 
  > ### ** Examples
  > 
  > {
  + cdm <- mockCohortCharacteristics()
  + 
  + result <- summariseCharacteristics(cdm$cohort1)
  + 
  + availablePlotColumns(result)
  + 
  + mockDisconnect(cdm)
  + }
  ℹ adding demographics columns
  Warning: Unknown or uninitialised column: `src`.
  Error in CDMConnector::dbms(dot$src$con) : 
    Assertion on 'con' failed: Must inherit from class 'DBIConnection', but has class 'NULL'.
  Calls: summariseCharacteristics ... <Anonymous> -> <Anonymous> -> makeAssertion -> mstop
  Execution halted

Package: CohortCharacteristics
Check: for code/documentation mismatches
New result: WARNING
  Codoc mismatches from Rd file 'mockCohortCharacteristics.Rd':
  mockCohortCharacteristics
    Code: function(numberIndividuals = 10, ..., source = "local", con =
                   lifecycle::deprecated(), writeSchema =
                   lifecycle::deprecated(), seed =
                   lifecycle::deprecated())
    Docs: function(con = NULL, writeSchema = NULL, numberIndividuals =
                   10, ..., seed = NULL)
    Argument names in code not in docs:
      source
    Mismatches in argument names (first 3):
      Position: 1 Code: numberIndividuals Docs: con
      Position: 2 Code: ... Docs: writeSchema
      Position: 3 Code: source Docs: numberIndividuals
    Mismatches in argument default values:
      Name: 'con' Code: lifecycle::deprecated() Docs: NULL
      Name: 'writeSchema' Code: lifecycle::deprecated() Docs: NULL
      Name: 'seed' Code: lifecycle::deprecated() Docs: NULL

Package: CohortCharacteristics
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [128s/65s]
  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(CohortCharacteristics)
    > 
    > test_check("CohortCharacteristics")
    Starting 2 test processes
    [ FAIL 16 | WARN 61 | SKIP 22 | PASS 92 ]
    
    ══ Skipped tests (22) ══════════════════════════════════════════════════════════
    • On CRAN (22): 'test-benchmarkCohortCharacteristics.R:2:3',
      'test-plotCharacteristics.R:2:3', 'test-plotCharacteristics.R:151:3',
      'test-plotCohortCount.R:2:3', 'test-plotCohortOverlap.R:2:3',
      'test-plotCohortTiming.R:2:3', 'test-plotCohortTiming.R:100:3',
      'test-summariseCharacteristics.R:1171:3',
      'test-summariseCharacteristics.R:1401:3',
      'test-summariseCharacteristics.R:1517:3', 'test-summariseCohortCount.R:2:3',
      'test-plotLargeScaleCharacteristics.R:3:3',
      'test-summariseLargeScaleCharacteristics.R:2:3', 'test-table.R:2:3',
      'test-tableCharacteristics.R:2:3', 'test-tableCharacteristics.R:120:3',
      'test-tableCohortAttrition.R:2:3', 'test-tableCohortCount.R:2:3',
      'test-tableCohortOverlap.R:2:3', 'test-tableCohortTiming.R:2:3',
      'test-tableLargeScaleCharacteristics.R:2:3',
      'test-tableLargeScaleCharacteristics.R:86:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-summariseCharacteristics.R:81:3'): test summariseCharacteristics ──
    Expected `... <- NULL` to run without any errors.
    i Actually got a <simpleError> with text:
      Assertion on 'con' failed: Must inherit from class 'DBIConnection', but has class 'NULL'.
    ── Error ('test-summariseCharacteristics.R:93:3'): test summariseCharacteristics ──
    Error in `eval(code, test_env)`: object 'result' not found
    Backtrace:
        ▆
     1. ├─testthat::expect_true(inherits(result, "summarised_result")) at test-summariseCharacteristics.R:93:3
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. └─base::inherits(result, "summarised_result")
    ── Failure ('test-summariseCharacteristics.R:435:3'): test empty cohort ────────
    Expected `... <- NULL` to run without any errors.
    i Actually got a <simpleError> with text:
      Assertion on 'con' failed: Must inherit from class 'DBIConnection', but has class 'NULL'.
    ── Error ('test-summariseCharacteristics.R:447:3'): test empty cohort ──────────
    Error in `eval(code, test_env)`: object 'res' not found
    Backtrace:
        ▆
     1. ├─testthat::expect_true(...) at test-summariseCharacteristics.R:447:3
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─base::unique(...)
     5. ├─dplyr::pull(...)
     6. └─dplyr::filter(res, variable_name == "Medications")
    ── Error ('test-summariseCharacteristics.R:557:3'): test cohort id ─────────────
    Error in `CDMConnector::dbms(dot$src$con)`: Assertion on 'con' failed: Must inherit from class 'DBIConnection', but has class 'NULL'.
    Backtrace:
         ▆
      1. ├─CohortCharacteristics::summariseCharacteristics(...) at test-summariseCharacteristics.R:557:3
      2. │ └─... %>% ...
      3. ├─dplyr::mutate(...)
      4. ├─omopgenerics:::mutate.cdm_table(...)
      5. │ ├─dplyr::mutate(.data, ...)
      6. │ └─dplyr:::mutate.data.frame(.data, ...)
      7. │   ├─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
      8. │   │ └─base::force(dots)
      9. │   └─dplyr:::dplyr_quosures(...)
     10. │     └─rlang::quos(..., .ignore_empty = "all")
     11. └─CDMConnector::datediff("cohort_start_date", "cohort_end_date")
     12.   └─CDMConnector::dbms(dot$src$con)
     13.     └─checkmate::assertClass(con, "DBIConnection")
     14.       └─checkmate::makeAssertion(x, res, .var.name, add)
     15.         └─checkmate:::mstop(...)
    ── Failure ('test-summariseCharacteristics.R:679:3'): arguments tableIntersect ──
    Expected `... <- NULL` to run without any errors.
    i Actually got a <simpleError> with text:
      Assertion on 'con' failed: Must inherit from class 'DBIConnection', but has class 'NULL'.
    ── Error ('test-summariseCharacteristics.R:691:3'): arguments tableIntersect ───
    Error in `eval(code, test_env)`: object 'results' not found
    Backtrace:
        ▆
     1. ├─testthat::expect_true(...) at test-summariseCharacteristics.R:691:3
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─"Number visits anytime before" %in% ...
     5. ├─results %>% dplyr::pull("variable_name")
     6. └─dplyr::pull(., "variable_name")
    ── Failure ('test-summariseCharacteristics.R:1008:3'): arguments cohortIntersect ──
    Expected `... <- NULL` to run without any errors.
    i Actually got a <simpleError> with text:
      Assertion on 'con' failed: Must inherit from class 'DBIConnection', but has class 'NULL'.
    ── Error ('test-summariseCharacteristics.R:1019:3'): arguments cohortIntersect ──
    Error in `eval(code, test_env)`: object 'results' not found
    Backtrace:
        ▆
     1. ├─testthat::expect_true(...) at test-summariseCharacteristics.R:1019:3
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─"Cohort 1 anytime before" %in% ...
     5. ├─results %>% dplyr::pull("variable_name")
     6. └─dplyr::pull(., "variable_name")
    ── Error ('test-summariseCharacteristics.R:1474:3'): arrange ageGroup ──────────
    Error in `CDMConnector::dbms(dot$src$con)`: Assertion on 'con' failed: Must inherit from class 'DBIConnection', but has class 'NULL'.
    Backtrace:
         ▆
      1. ├─CohortCharacteristics::summariseCharacteristics(...) at test-summariseCharacteristics.R:1474:3
      2. │ └─... %>% ...
      3. ├─dplyr::mutate(...)
      4. ├─omopgenerics:::mutate.cdm_table(...)
      5. │ ├─dplyr::mutate(.data, ...)
      6. │ └─dplyr:::mutate.data.frame(.data, ...)
      7. │   ├─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
      8. │   │ └─base::force(dots)
      9. │   └─dplyr:::dplyr_quosures(...)
     10. │     └─rlang::quos(..., .ignore_empty = "all")
     11. └─CDMConnector::datediff("cohort_start_date", "cohort_end_date")
     12.   └─CDMConnector::dbms(dot$src$con)
     13.     └─checkmate::assertClass(con, "DBIConnection")
     14.       └─checkmate::makeAssertion(x, res, .var.name, add)
     15.         └─checkmate:::mstop(...)
    ── Failure ('test-summariseCharacteristics.R:1606:3'): weights in summariseCharacteristics ──
    Expected `... <- NULL` to run without any errors.
    i Actually got a <simpleError> with text:
      Assertion on 'con' failed: Must inherit from class 'DBIConnection', but has class 'NULL'.
    ── Failure ('test-summariseCharacteristics.R:1615:3'): weights in summariseCharacteristics ──
    Expected `... <- NULL` to run without any errors.
    i Actually got a <simpleError> with text:
      Assertion on 'con' failed: Must inherit from class 'DBIConnection', but has class 'NULL'.
    ── Error ('test-summariseCharacteristics.R:1627:3'): weights in summariseCharacteristics ──
    Error in `eval(code, test_env)`: object 'result' not found
    Backtrace:
        ▆
     1. └─testthat::expect_identical(...) at test-summariseCharacteristics.R:1627:3
     2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
     3.     └─rlang::eval_bare(expr, quo_get_env(quo))
    ── Failure ('test-summariseCohortCodelist.R:53:3'): test summarise cohortCodelist attribute ──
    dplyr::as_tibble(omopgenerics::tidy(res)) (`actual`) not identical to `expected` (`expected`).
    
    actual vs expected
                               cdm_name
    - actual[1, ]   PatientProfilesMock
    + expected[1, ] PP_MOCK            
    - actual[2, ]   PatientProfilesMock
    + expected[2, ] PP_MOCK            
    - actual[3, ]   PatientProfilesMock
    + expected[3, ] PP_MOCK            
    - actual[4, ]   PatientProfilesMock
    + expected[4, ] PP_MOCK            
    - actual[5, ]   PatientProfilesMock
    + expected[5, ] PP_MOCK            
    - actual[6, ]   PatientProfilesMock
    + expected[6, ] PP_MOCK            
    - actual[7, ]   PatientProfilesMock
    + expected[7, ] PP_MOCK            
    
        actual$cdm_name       | expected$cdm_name    
    [1] "PatientProfilesMock" - "PP_MOCK"         [1]
    [2] "PatientProfilesMock" - "PP_MOCK"         [2]
    [3] "PatientProfilesMock" - "PP_MOCK"         [3]
    [4] "PatientProfilesMock" - "PP_MOCK"         [4]
    [5] "PatientProfilesMock" - "PP_MOCK"         [5]
    [6] "PatientProfilesMock" - "PP_MOCK"         [6]
    [7] "PatientProfilesMock" - "PP_MOCK"         [7]
    ── Error ('test-summariseCohortOverlap.R:246:3'): test countBy ─────────────────
    Error in `validateGeneratedCohortSet(cohort, soft = .softValidation)`: ! There is overlap between entries in the cohort, 2 overlaps detected for subject_id 1 and 1
    Backtrace:
        ▆
     1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCohortOverlap.R:246:3
     2.   └─omopgenerics::cdmFromTables(...)
     3.     └─omopgenerics::newCohortTable(...)
     4.       └─omopgenerics:::validateGeneratedCohortSet(cohort, soft = .softValidation)
     5.         └─omopgenerics::validateCohortArgument(...)
     6.           └─omopgenerics:::checkOverlap(...)
     7.             └─cli::cli_abort(...)
     8.               └─rlang::abort(...)
    ── Error ('test-summariseCohortTiming.R:40:3'): summariseCohortTiming ──────────
    Error in `CDMConnector::dbms(dot$src$con)`: Assertion on 'con' failed: Must inherit from class 'DBIConnection', but has class 'NULL'.
    Backtrace:
         ▆
      1. ├─CohortCharacteristics::summariseCohortTiming(cdm$table, restrictToFirstEntry = TRUE) at test-summariseCohortTiming.R:40:3
      2. │ ├─dplyr::collect(...)
      3. │ ├─dplyr::select(...)
      4. │ └─... %>% ...
      5. ├─dplyr::mutate(...)
      6. ├─omopgenerics:::mutate.cdm_table(...)
      7. │ ├─dplyr::mutate(.data, ...)
      8. │ └─dplyr:::mutate.data.frame(.data, ...)
      9. │   ├─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
     10. │   │ └─base::force(dots)
     11. │   └─dplyr:::dplyr_quosures(...)
     12. │     └─rlang::quos(..., .ignore_empty = "all")
     13. └─CDMConnector::datediff(...)
     14.   └─CDMConnector::dbms(dot$src$con)
     15.     └─checkmate::assertClass(con, "DBIConnection")
     16.       └─checkmate::makeAssertion(x, res, .var.name, add)
     17.         └─checkmate:::mstop(...)
    
    [ FAIL 16 | WARN 61 | SKIP 22 | PASS 92 ]
    Error: Test failures
    Execution halted