Last updated on 2025-12-07 07:50:37 CET.
| Package | ERROR | WARN | NOTE | OK |
|---|---|---|---|---|
| CohortCharacteristics | 2 | 2 | 9 | |
| DrugUtilisation | 1 | 1 | 11 | |
| OmopConstructor | 1 | 12 | ||
| omopgenerics | 1 | 1 | 11 | |
| OmopViewer | 1 | 12 | ||
| PatientProfiles | 2 | 11 |
Current CRAN status: ERROR: 2, NOTE: 2, OK: 9
Version: 1.1.0
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'visOmopResults', 'covr', 'DiagrammeR', 'DT', 'flextable', 'gt',
'Hmisc', 'knitr', 'plotly', 'reactable', 'rmarkdown', 'spelling'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [345s/221s]
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 computed:
> 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 2025-12-06 12:28:53.267028
> test-plotCohortTiming.R: v Summary finished, at 2025-12-06 12:28:53.496848
> test-plotCohortTiming.R: `result_id` is not present in result.
Saving _problems/test-plotCohortTiming-237.R
Saving _problems/test-plotCohortAttrition-14.R
> 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-summariseCharacteristics.R: i adding demographics columns
> test-plotLargeScaleCharacteristics.R: v Summarising large scale characteristics
> 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
Saving _problems/test-summariseCohortCodelist-9.R
> 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-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-summariseCohortOverlap.R: `result_id` is not present in result.
> 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-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-summariseCohortOverlap.R: `result_id` is not present in result.
> 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-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: * `-365 to 0` -> `365_to_0`
> test-summariseCharacteristics.R: i summarising data
> test-summariseCharacteristics.R: i summarising cohort cohort_1
> test-summariseCohortTiming.R: i The following estimates will be computed:
> 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 2025-12-06 12:30:25.466697
> test-summariseCohortTiming.R: v Summary finished, at 2025-12-06 12:30:25.835655
> test-summariseCharacteristics.R: i summarising cohort cohort_2
> test-summariseCohortTiming.R: i The following estimates will be computed:
> test-summariseCohortTiming.R: * days_between_cohort_entries: min, max
> test-summariseCohortTiming.R: > Start summary of data, at 2025-12-06 12:30:26.791567
> test-summariseCohortTiming.R: v Summary finished, at 2025-12-06 12:30:26.952665
> test-summariseCharacteristics.R: i summarising cohort cohort_3
> test-summariseCohortTiming.R: i The following estimates will be computed:
> test-summariseCohortTiming.R: * days_between_cohort_entries: 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 2025-12-06 12:30:27.92438
> test-summariseCohortTiming.R: v Summary finished, at 2025-12-06 12:30:28.351087
> test-summariseCharacteristics.R: v summariseCharacteristics finished!
> test-summariseCohortTiming.R: i The following estimates will be computed:
> 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 2025-12-06 12:30:31.358878
> test-summariseCohortTiming.R: v Summary finished, at 2025-12-06 12:30:32.743473
> test-summariseCohortTiming.R: i The following estimates will be computed:
> test-summariseCohortTiming.R: * days_between_cohort_entries: 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 2025-12-06 12:30:34.419245
> test-summariseCohortTiming.R: v Summary finished, at 2025-12-06 12:30:35.449546
> 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-summariseCohortTiming.R: i The following estimates will be computed:
> 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 2025-12-06 12:30:43.537426
> 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-summariseCohortTiming.R: v Summary finished, at 2025-12-06 12:30:44.426939
> test-summariseCharacteristics.R: i summarising data
> test-utilities.R: `group` is not present in settings.
> test-summariseCharacteristics.R: i summarising cohort exposed
> test-utilities.R: `group` is not present in settings.
> test-utilities.R: `group` is not present in settings.
> 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
Saving _problems/test-summariseCharacteristics-1662.R
Saving _problems/test-summariseCharacteristics-1668.R
[ FAIL 5 | WARN 8 | SKIP 24 | PASS 196 ]
══ 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:107:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plotCohortTiming.R:237:3'): plotCohortTiming, density x axis ───
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `plotInternal(result = result, resultType = "summarise_cohort_timing", plotType = plotType, facet = facet, colour = colour, uniqueCombinations = uniqueCombinations, oneVariable = TRUE, toYears = timeScale == "years", excludeGroup = "variable_level", style = style)`: The package "visOmopResults" is required.
Backtrace:
▆
1. ├─testthat::expect_warning(p <- plotCohortTiming(timing, plotType = "densityplot")) at test-plotCohortTiming.R:237:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─CohortCharacteristics::plotCohortTiming(timing, plotType = "densityplot")
8. └─CohortCharacteristics:::plotInternal(...)
9. └─rlang::check_installed("visOmopResults")
── Error ('test-plotCohortAttrition.R:14:3'): plot cohort attrition ────────────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `plotCohortAttrition(ca, cohortId = 2)`: The package "DiagrammeR" is required.
Backtrace:
▆
1. ├─testthat::expect_warning(x <- plotCohortAttrition(ca, cohortId = 2)) at test-plotCohortAttrition.R:14:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─CohortCharacteristics::plotCohortAttrition(ca, cohortId = 2)
8. └─rlang::check_installed("DiagrammeR")
── Error ('test-summariseCohortCodelist.R:9:3'): test summarise cohortCodelist attribute ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `tableCohortCodelist(res)`: The package "reactable" is required.
Backtrace:
▆
1. ├─testthat::expect_warning(tableCohortCodelist(res)) at test-summariseCohortCodelist.R:9:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─CohortCharacteristics::tableCohortCodelist(res)
8. └─rlang::check_installed("reactable")
── Failure ('test-summariseCharacteristics.R:1653:3'): weights in summariseCharacteristics ──
Expected `... <- NULL` not to throw any errors.
Actually got a <purrr_error_indexed> with message:
i In index: 1.
Caused by error in `PatientProfiles::summariseResult()`:
! The package "Hmisc" is required.
── Error ('test-summariseCharacteristics.R:1665:3'): weights in summariseCharacteristics ──
Error in `eval(code, test_env)`: object 'resultW' not found
Backtrace:
▆
1. └─testthat::expect_identical(...) at test-summariseCharacteristics.R:1665:3
2. └─testthat::quasi_label(enquo(expected), expected.label)
3. └─rlang::eval_bare(expr, quo_get_env(quo))
[ FAIL 5 | WARN 8 | SKIP 24 | PASS 196 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.0
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.0
Check: installed package size
Result: NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
doc 4.3Mb
help 1.8Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-windows-x86_64
Version: 1.1.0
Check: package dependencies
Result: ERROR
Package required and available but unsuitable version: ‘omopgenerics’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64
Current CRAN status: ERROR: 1, WARN: 1, OK: 11
Version: 1.0.5
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'covr', 'flextable', 'gt', 'knitr', 'rmarkdown', 'visOmopResults'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.5
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.5
Check: package dependencies
Result: ERROR
Package required and available but unsuitable version: ‘omopgenerics’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64
Current CRAN status: WARN: 1, OK: 12
Version: 0.1.0
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'bookdown', 'gt', 'knitr', 'rmarkdown', 'visOmopResults'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 1, WARN: 1, OK: 11
Version: 1.3.4
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'covr', 'gt', 'knitr', 'rmarkdown'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.4
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.4
Check: package dependencies
Result: ERROR
Package required and available but unsuitable version: ‘dbplyr’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64
Current CRAN status: ERROR: 1, OK: 12
Version: 0.5.0
Check: package dependencies
Result: ERROR
Packages required but not available:
'DT', 'gt', 'usethis', 'visOmopResults', 'yaml'
Packages suggested but not available for checking:
'devtools', 'DiagrammeR', 'htmlwidgets', 'knitr', 'plotly',
'reactable', 'rmarkdown', 'rsconnect', 'shinyTree', 'sortable'
VignetteBuilder package required for checking but not installed: ‘knitr’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 2, OK: 11
Version: 1.4.4
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'covr', 'DT', 'gt', 'Hmisc', 'knitr', 'rmarkdown', 'spelling'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.4.4
Check: tests
Result: ERROR
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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.4.4
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.4.4
Check: package dependencies
Result: ERROR
Package required and available but unsuitable version: ‘omopgenerics’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64