Check results for 'CohortCharacteristics'

using R version 4.4.3 Patched (2026-02-12 r89426 ucrt)
using platform: x86_64-w64-mingw32
R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0
running under: Windows Server 2022 x64 (build 20348)
using session charset: UTF-8
checking for file 'CohortCharacteristics/DESCRIPTION' ... OK
checking extension type ... Package
this is package 'CohortCharacteristics' version '1.1.1'
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking whether package 'CohortCharacteristics' can be installed ... OK See the install log for details.
checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: doc 3.6Mb help 1.8Mb
checking package directory ... OK
checking 'build' directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [1s] OK
checking whether the package can be loaded with stated dependencies ... [1s] OK
checking whether the package can be unloaded cleanly ... [1s] OK
checking whether the namespace can be loaded with stated dependencies ... [1s] OK
checking whether the namespace can be unloaded cleanly ... [1s] OK
checking loading without being on the library search path ... [1s] OK
checking use of S3 registration ... OK
checking dependencies in R code ... OK
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checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [11s] OK
checking Rd files ... [1s] OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking installed files from 'inst/doc' ... OK
checking files in 'vignettes' ... OK
checking examples ... [17s] OK
checking for unstated dependencies in 'tests' ... OK
checking tests ... [394s] ERROR Running 'spelling.R' [0s] Running 'testthat.R' [393s] 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 2026-03-19 01:59:11.523231 > test-plotCohortTiming.R: v Summary finished, at 2026-03-19 01:59:11.813405 > 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 2026-03-19 01:59:24.87757 > test-plotCohortAttrition.R: v Summary finished, at 2026-03-19 01:59:25.068085 > 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-summariseCharacteristics.R: i summarising data > test-summariseCharacteristics.R: i summarising cohort exposed > test-summariseCohortOverlap.R: Cohort table is empty: returning empty summarised result. > 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-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-summariseCohortOverlap.R: `result_id` is not present in result. > 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 2026-03-19 02:02:18.776398 > test-summariseCohortTiming.R: v Summary finished, at 2026-03-19 02:02:19.429558 > 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 2026-03-19 02:02:32.431835 > 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: v Summary finished, at 2026-03-19 02:02:33.664813 Saving _problems/test-summariseCohortTiming-63.R > test-utilities.R: `group` is not present in settings. > test-summariseCharacteristics.R: i adding cohortIntersectFlag 2/2 > test-utilities.R: `group` is not present in settings. > test-summariseCharacteristics.R: window names casted to snake_case: > test-summariseCharacteristics.R: * `-Inf to 0` -> `inf_to_0` > test-utilities.R: `group` is not present in settings. > 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 17 | 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 17 | SKIP 24 | PASS 218 ] Error: ! Test failures. Execution halted
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [269s] OK
checking PDF version of manual ... [20s] OK
checking HTML version of manual ... [7s] OK
DONE

Status: 1 ERROR, 1 NOTE