Running 'spelling.R' [0s]
  Running 'testthat.R' [401s]
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.
  > test-plotCohortTiming.R: i The following estimates will be calculated:
  > test-plotCohortTiming.R: * days_between_cohort_entries: min, q25, median, q75, max, density
  > test-plotCohortTiming.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-plotCohortTiming.R: > Start summary of data, at 2026-03-17 09:29:55.211308
  > test-plotCohortTiming.R: v Summary finished, at 2026-03-17 09:29:55.602913
  > test-plotCohortTiming.R: `result_id` is not present in result.
  > test-plotCohortTiming.R: `result_id` is not present in result.
  > test-plotCohortTiming.R: `result_id` is not present in result.
  > test-plotCohortTiming.R: `result_id` is not present in result.
  Saving _problems/test-plotCohortTiming-245.R
  > test-plotCohortAttrition.R: i The following estimates will be calculated:
  > test-plotCohortAttrition.R: * cohort_end_date: min, q25, median, q75, max
  > test-plotCohortAttrition.R: * cohort_start_date: min, q25, median, q75, max
  > test-plotCohortAttrition.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-plotCohortAttrition.R: > Start summary of data, at 2026-03-17 09:30:10.346178
  > test-plotCohortAttrition.R: v Summary finished, at 2026-03-17 09:30:10.514136
  > test-plotLargeScaleCharacteristics.R: i Summarising large scale characteristics 
  > test-plotLargeScaleCharacteristics.R:  - getting characteristics from table condition_occurrence (1 of 1)
  > test-plotLargeScaleCharacteristics.R:  - getting characteristics from table condition_occurrence (1 of 1) for time ...
  > test-plotLargeScaleCharacteristics.R:  - getting characteristics from table condition_occurrence (1 of 1) for time ...
  > test-plotLargeScaleCharacteristics.R:  - getting characteristics from table condition_occurrence (1 of 1) for time ...
  > test-plotLargeScaleCharacteristics.R:  - getting characteristics from table condition_occurrence (1 of 1) for time ...
  > test-plotLargeScaleCharacteristics.R:  - getting characteristics from table condition_occurrence (1 of 1) for time ...
  > test-plotLargeScaleCharacteristics.R:  - getting characteristics from table condition_occurrence (1 of 1) for time ...
  > test-plotLargeScaleCharacteristics.R:  - getting characteristics from table condition_occurrence (1 of 1) for time ...
  > test-plotLargeScaleCharacteristics.R: Formatting result
  > test-plotLargeScaleCharacteristics.R: v Summarising large scale characteristics
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 1/2
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-365 to 0` -> `365_to_0`
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 2/2
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-Inf to 0` -> `inf_to_0`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 1/3
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 2/3
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 3/3
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-Inf to 0` -> `inf_to_0`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 1/1
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-365 to 0` -> `365_to_0`
  > test-summariseCohortOverlap.R: Cohort table is empty: returning empty summarised result.
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 1/1
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-365 to 0` -> `365_to_0`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 1/1
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 1/1
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 1/1
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 1/2
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-365 to 0` -> `365_to_0`
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 2/2
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-Inf to 0` -> `inf_to_0`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort cohort_1
  > test-summariseCharacteristics.R: i summarising cohort cohort_2
  > test-summariseCharacteristics.R: i summarising cohort cohort_3
  > test-summariseCohortOverlap.R: `result_id` is not present in result.
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCohortOverlap.R: `result_id` is not present in result.
  > test-summariseCharacteristics.R: i adding tableIntersectFlag 1/1
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-365 to 0` -> `365_to_0`
  > test-summariseCohortOverlap.R: `result_id` is not present in result.
  > test-summariseCohortOverlap.R: `result_id` is not present in result.
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort cohort_1
  > test-summariseCohortOverlap.R: `result_id` is not present in result.
  > test-summariseCharacteristics.R: i summarising cohort cohort_2
  > test-summariseCharacteristics.R: i summarising cohort cohort_3
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCohortTiming.R: Cohort table is empty: returning empty summarised timing result.
  > test-summariseCohortTiming.R: i The following estimates will be calculated:
  > test-summariseCohortTiming.R: * days_between_cohort_entries: min, q25, median, q75, max, density
  > test-summariseCohortTiming.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseCohortTiming.R: > Start summary of data, at 2026-03-17 09:33:03.125755
  > test-summariseCohortTiming.R: v Summary finished, at 2026-03-17 09:33:03.751014
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCohortTiming.R: i The following estimates will be calculated:
  > test-summariseCohortTiming.R: * days_between_cohort_entries: min, q25, median, q75, max
  > test-summariseCohortTiming.R: ! Table is collected to memory as not all requested estimates are supported on the database side
  > test-summariseCohortTiming.R: > Start summary of data, at 2026-03-17 09:33:16.489483
  > test-summariseCohortTiming.R: v Summary finished, at 2026-03-17 09:33:17.858308
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 1/2
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-365 to 0` -> `365_to_0`
  Saving _problems/test-summariseCohortTiming-63.R
  > test-utilities.R: `group` is not present in settings.
  > test-utilities.R: `group` is not present in settings.
  > test-utilities.R: `group` is not present in settings.
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 2/2
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-Inf to 0` -> `inf_to_0`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 1/2
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-365 to 0` -> `365_to_0`
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 2/2
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-Inf to 0` -> `inf_to_0`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding tableIntersectCount 1/1
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-Inf to -1` -> `inf_to_1`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding tableIntersectFlag 1/1
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-Inf to -1` -> `inf_to_1`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding tableIntersectDate 1/1
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-Inf to -1` -> `inf_to_1`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding tableIntersectDays 1/1
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `1 to Inf` -> `1_to_inf`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort exposed
  > test-summariseCharacteristics.R: i summarising cohort unexposed
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding cohortIntersectCount 1/1
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-Inf to -1` -> `inf_to_1`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort cohort_1
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 1/1
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-Inf to -1` -> `inf_to_1`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort cohort_1
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding cohortIntersectDate 1/1
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-Inf to -1` -> `inf_to_1`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort cohort_1
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding cohortIntersectDays 1/1
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `1 to Inf` -> `1_to_inf`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort cohort_1
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort cohort_1
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort cohort_1
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort cohort_1
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort cohort_1
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 1/1
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-365 to -1` -> `365_to_1`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort cohort_1
  > test-summariseCharacteristics.R: i summarising cohort cohort_2
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  > test-summariseCharacteristics.R: i adding demographics columns
  > test-summariseCharacteristics.R: i adding cohortIntersectFlag 1/1
  > test-summariseCharacteristics.R: window names casted to snake_case:
  > test-summariseCharacteristics.R: * `-365 to -1` -> `365_to_1`
  > test-summariseCharacteristics.R: i summarising data
  > test-summariseCharacteristics.R: i summarising cohort cohort_1
  > test-summariseCharacteristics.R: i summarising cohort cohort_2
  > test-summariseCharacteristics.R: v summariseCharacteristics finished!
  [ FAIL 2 | WARN 18 | SKIP 24 | PASS 218 ]
  
  ══ Skipped tests (24) ══════════════════════════════════════════════════════════
  • On CRAN (22): 'test-benchmarkCohortCharacteristics.R:2:3',
    'test-plotCharacteristics.R:2:3', 'test-plotCharacteristics.R:176:3',
    'test-plotCohortCount.R:2:3', 'test-plotCohortOverlap.R:2:3',
    'test-plotCohortTiming.R:2:3', 'test-plotCohortTiming.R:100:3',
    'test-plotLargeScaleCharacteristics.R:3:3',
    'test-summariseCohortCount.R:2:3',
    'test-summariseLargeScaleCharacteristics.R:2:3', 'test-table.R:2:3',
    'test-tableCharacteristics.R:2:3', 'test-tableCharacteristics.R:124:3',
    '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:80:3',
    'test-summariseCharacteristics.R:1180:3',
    'test-summariseCharacteristics.R:1425:3',
    'test-summariseCharacteristics.R:1552:3'
  • empty test (2): 'test-plotLargeScaleCharacteristics.R:140:1',
    'test-summariseCohortTiming.R:114:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plotCohortTiming.R:245:3'): plotCohortTiming, density x axis ───
  Error in `dplyr::collect(x)`: Failed to collect lazy table.
  Caused by error in `dbSendQuery()`:
  ! INTERNAL Error: Failed to bind column reference "cohort_start_date_comparator" [24.0]: inequal types (DATE != INTEGER)
  This error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.
  For more information, see https://duckdb.org/docs/stable/dev/internal_errors
  i Context: rapi_prepare
  i Error type: INTERNAL
  ── Error ('test-summariseCohortTiming.R:60:3'): summariseCohortTiming ──────────
  Error in `dplyr::collect(x)`: Failed to collect lazy table.
  Caused by error in `dbSendQuery()`:
  ! INTERNAL Error: Failed to bind column reference "cohort_start_date_comparator" [24.0]: inequal types (DATE != INTEGER)
  This error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.
  For more information, see https://duckdb.org/docs/stable/dev/internal_errors
  i Context: rapi_prepare
  i Error type: INTERNAL
  
  [ FAIL 2 | WARN 18 | SKIP 24 | PASS 218 ]
  Error:
  ! Test failures.
  Execution halted