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Type 'q()' to quit R. > # 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/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(omopgenerics) Attaching package: 'omopgenerics' The following object is masked from 'package:stats': filter > > test_check("omopgenerics") Starting 2 test processes. > test-classCodelist.R: > test-classCodelist.R: > test-classCodelist.R: - disease (3 codes) > test-classCodelist.R: -- 1 codelist ------------------------------------------------------------------ > test-classCodelist.R: > test-classCodelist.R: -- 2 codelists ----------------------------------------------------------------- > test-classCodelist.R: > test-classCodelist.R: - disease X (3 codes) > test-classCodelist.R: - disease Y (2 codes) > test-classCodelistWithDetails.R: > test-classCodelistWithDetails.R: -- 1 codelist with details ----------------------------------------------------- > test-classCodelistWithDetails.R: > test-classCodelistWithDetails.R: - disease (3 codes) > test-classCodelistWithDetails.R: > test-classCodelistWithDetails.R: -- 2 codelists with details ---------------------------------------------------- > test-classCodelistWithDetails.R: > test-classCodelistWithDetails.R: - disease X (3 codes) > test-classCodelistWithDetails.R: - disease Y (2 codes) > test-classCodelist.R: i Element `2` converted to ``. > test-classCodelist.R: ! Element `2` eliminated as could not be converted to ``. > test-classSummarisedResult.R: ! `result_type`, `package_name`, and `package_version` moved to settings. This is not recommended as settings should be explicitly provided. > test-classSummarisedResult.R: i NOTE that this can cause problems with settings. > test-classSummarisedResult.R: ! `result_type`, `package_name`, and `package_version` moved to settings. This is not recommended as settings should be explicitly provided. > test-classSummarisedResult.R: i NOTE that this can cause problems with settings. > test-classSummarisedResult.R: ! `result_type`, `package_name`, and `package_version` moved to settings. This is not recommended as settings should be explicitly provided. > test-classSummarisedResult.R: i NOTE that this can cause problems with settings. > test-classSummarisedResult.R: ! `result_type`, `package_name`, and `package_version` moved to settings. This is not recommended as settings should be explicitly provided. > test-classSummarisedResult.R: i NOTE that this can cause problems with settings. > test-classSummarisedResult.R: ! `result_type`, `package_name`, and `package_version` moved to settings. This is not recommended as settings should be explicitly provided. > test-classSummarisedResult.R: i NOTE that this can cause problems with settings. > test-classSummarisedResult.R: ! `result_type`, `package_name`, and `package_version` moved to settings. This is not recommended as settings should be explicitly provided. > test-classSummarisedResult.R: i NOTE that this can cause problems with settings. > test-classSummarisedResult.R: ! `result_type`, `package_name`, and `package_version` moved to settings. This is not recommended as settings should be explicitly provided. > test-classSummarisedResult.R: i NOTE that this can cause problems with settings. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-classSummarisedResult.R: ! 6 duplicated rows eliminated. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-classSummarisedResult.R: ! 6 duplicated rows eliminated. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-classSummarisedResult.R: ! 2 duplicated rows eliminated. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-classSummarisedResult.R: ! `result_type`, `package_name`, and `package_version` moved to settings. This is not recommended as settings should be explicitly provided. > test-classSummarisedResult.R: i NOTE that this can cause problems with settings. > test-classSummarisedResult.R: ! `result_type`, `package_name`, and `package_version` moved to settings. This is not recommended as settings should be explicitly provided. > test-classSummarisedResult.R: i NOTE that this can cause problems with settings. > test-classSummarisedResult.R: `package_name` and `package_version` added to settings. > test-classSummarisedResult.R: `param_to_eliminate` eliminated from settings as all elements are NA. > test-classSummarisedResult.R: i Column `cdm_name` created as 'unknown' as not present in x. > test-classSummarisedResult.R: i Column `variable_level` created as 'overall' as not present in x. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-classSummarisedResult.R: i Column `cdm_name` created as 'unknown' as not present in x. > test-classSummarisedResult.R: i Column `variable_level` created as 'overall' as not present in x. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-classSummarisedResult.R: i Column `cdm_name` created as 'unknown' as not present in x. > test-classSummarisedResult.R: i Column `variable_level` created as 'overall' as not present in x. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-classSummarisedResult.R: i Column `cdm_name` created as 'unknown' as not present in x. > test-classSummarisedResult.R: i Column `variable_name` created as 'overall' as not present in x. > test-classSummarisedResult.R: i Column `variable_level` created as 'overall' as not present in x. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-classSummarisedResult.R: i Column `cdm_name` created as 'unknown' as not present in x. > test-classSummarisedResult.R: i Column `variable_level` created as 'overall' as not present in x. > test-classSummarisedResult.R: `result_type`, `package_name`, and `package_version` added to settings. > test-exportSummarisedResult.R: `min_cell_count` casted to character. > test-emptyObjects.R: `result_type`, `package_name`, and `package_version` added to settings. > test-emptyObjects.R: `my_setting` casted to character. > test-importCodelist.R: 2 codelists imported. > test-importCodelist.R: 1 codelist imported. > test-importCodelist.R: 2 codelists imported. > test-importConceptSetExpression.R: 2 concept set expressions imported. > test-importConceptSetExpression.R: 2 concept set expressions imported. > test-importConceptSetExpression.R: 0 concept set expressions imported. > test-filter.R: `result_type`, `package_name`, and `package_version` added to settings. > test-importConceptSetExpression.R: 2 concept set expressions imported. > test-importConceptSetExpression.R: 2 concept set expressions imported. > test-importConceptSetExpression.R: 2 concept set expressions imported. > test-importConceptSetExpression.R: 0 concept set expressions imported. > test-filter.R: `result_type`, `package_name`, and `package_version` added to settings. > test-importConceptSetExpression.R: 2 concept set expressions imported. > test-filter.R: `result_type`, `package_name`, and `package_version` added to settings. > test-filter.R: `result_type`, `package_name`, and `package_version` added to settings. > test-logger.R: [2025-12-10 17:06:57] - gjkd > test-logger.R: i Creating log file: 'D:\temp\2025_12_10_17_05_17_24617\RtmpCOktPl\filedcc40534cc.txt'. > test-logger.R: [2025-12-10 17:06:57] - Log file created > test-logger.R: [2025-12-10 17:06:57] - Start analysis > test-logger.R: [2025-12-10 17:06:57] - Exporting log file > test-logger.R: ! Overwriting current log file > test-logger.R: i Creating log file: 'D:\temp\2025_12_10_17_05_17_24617\RtmpCOktPl\filedcc140a17cc.txt'. > test-logger.R: [2025-12-10 17:06:57] - Log file created > test-logger.R: ! Overwriting current log file > test-logger.R: ! Deleting prior existing log file: 'D:\temp\2025_12_10_17_05_17_24617\RtmpCOktPl\filedcc140a17cc.txt'. > test-logger.R: i Creating log file: 'D:\temp\2025_12_10_17_05_17_24617\RtmpCOktPl\filedcc140a17cc.txt'. > test-logger.R: [2025-12-10 17:06:57] - Log file created > test-logger.R: [2025-12-10 17:06:57] - gjkd > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_1.csv'. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_2.csv'. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_1.csv'. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_2.csv'. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_1.csv'. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_2.csv'. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_1.csv'. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_2.csv'. > test-methodBind.R: `result_type`, `package_name`, and `package_version` added to settings. > test-methodBind.R: `package_name` and `package_version` added to settings. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/og_012_1765382820/result_3.csv'. > test-methodBind.R: `package_name` and `package_version` added to settings. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_1.csv'. > test-methodBind.R: `param` casted to character. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_2.csv'. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/og_012_1765382820/result_3.csv'. > test-methodBind.R: `package_name` and `package_version` added to settings. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_1.csv'. > test-methodBind.R: `result_type`, `package_name`, and `package_version` added to settings. > test-methodBind.R: `washout` casted to character. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_2.csv'. > test-methodBind.R: ! 4 duplicated rows eliminated. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_1.csv'. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_2.csv'. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/og_012_1765382820/result_3.csv'. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_1.csv'. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_2.csv'. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/og_012_1765382820/result_3.csv'. > test-methodBind.R: `result_type`, `package_name`, and `package_version` added to settings. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818//result_1.csv'. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818//result_1.csv'. > test-methodBind.R: `result_type`, `package_name`, and `package_version` added to settings. > test-methodBind.R: `result_type`, `package_name`, and `package_version` added to settings. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818//result_1.csv'. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818//result_2.csv'. > test-methodBind.R: `result_type`, `package_name`, and `package_version` added to settings. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818//result_1.csv'. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818//result_2.csv'. > test-methodBind.R: `result_type`, `package_name`, and `package_version` added to settings. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_1.csv'. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_2.csv'. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818//result_1.csv'. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_1.csv'. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818/result_2.csv'. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_010_1765382818//result_1.csv'. > test-importSummarisedResult.R: ! 1 duplicated row eliminated. > test-importSummarisedResult.R: Reading file: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_011_1765382819/cars.csv'. > test-importSummarisedResult.R: Converting to summarised_result: 'D:\temp\2025_12_10_17_05_17_24617\Rtmp4gQd02/og_011_1765382819/cars.csv'. > test-importSummarisedResult.R: x Failed to convert because: > test-importSummarisedResult.R: Error in `omopgenerics::newSummarisedResult()`: x `x` must have result_id, cdm_name, group_name, group_level, strata_name, strata_level, variable_name, variable_level, estimate_name, estimate_type, estimate_value, additional_name, and additional_level as columns. ! `x` must be a table of class: ; it can not be NULL; must contain result_id, cdm_name, group_name, group_level, strata_name, strata_level, variable_name, variable_level, estimate_name, estimate_type, estimate_value, additional_name, and additional_level as columns. > test-methodSuppress.R: `min_cell_count` casted to character. > test-methodSuppress.R: `min_cell_count` casted to character. > test-methodSuppress.R: `min_cell_count` casted to character. > test-methodSuppress.R: `min_cell_count` casted to character. > test-methodSummary.R: `cohort_definition_id` casted to character. > test-methodSummary.R: `cohort_definition_id` casted to character. > test-methodSuppress.R: `min_cell_count` casted to character. > test-methodSummary.R: `cohort_definition_id` casted to character. > test-methodSuppress.R: `min_cell_count` casted to character. > test-methodSummary.R: `cohort_definition_id` casted to character. > test-methodSuppress.R: `min_cell_count` casted to character. > test-methodSummary.R: `cohort_definition_id` and `parameter` casted to character. > test-methodSuppress.R: `min_cell_count` casted to character. > test-methodSummary.R: `cohort_definition_id` and `parameter` casted to character. > test-methodSuppress.R: `min_cell_count` casted to character. > test-methodSummary.R: `cohort_definition_id` and `parameter` casted to character. > test-methodSummary.R: `cohort_definition_id` and `parameter` casted to character. > test-methodSuppress.R: `result_type`, `package_name`, and `package_version` added to settings. > test-methodTidy.R: ! 126 duplicated rows eliminated. > test-methodSuppress.R: `result_type`, `package_name`, and `package_version` added to settings. > test-omopDataFolder.R: i Creating 'D:\temp\2025_12_10_17_05_17_24617\RtmpCOktPl/OMOP_DATA'. > test-methodSuppress.R: `result_type`, `package_name`, and `package_version` added to settings. > test-methodSuppress.R: `result_type`, `package_name`, and `package_version` added to settings. > test-split.R: `group` is not present in settings. > test-split.R: `group` is not present in settings. > test-split.R: `group` is not present in settings. > test-split.R: `group` is not present in settings. > test-split.R: `x` is not present in settings. > test-split.R: `x` is not present in settings. > test-split.R: `group` is not present in settings. > test-split.R: `group` is not present in settings. > test-split.R: `result_type`, `package_name`, and `package_version` added to settings. > test-split.R: `package_name` and `package_version` added to settings. > test-split.R: `strata` is not present in settings. > test-split.R: `additional` is not present in settings. > test-unite.R: `result_type`, `package_name`, and `package_version` added to settings. > test-validate.R: window names casted to snake_case: > test-validate.R: * `-Inf to -1` -> `inf_to_1` > test-utilities.R: ! `result_type`, `package_name`, and `package_version` moved to settings. This is not recommended as settings should be explicitly provided. > test-utilities.R: i NOTE that this can cause problems with settings. > test-utilities.R: v PatientProfiles: 0.4.0 > test-utilities.R: ! `result_type`, `package_name`, and `package_version` moved to settings. This is not recommended as settings should be explicitly provided. > test-utilities.R: i NOTE that this can cause problems with settings. > test-validate.R: ! `result_type`, `package_name`, and `package_version` moved to settings. This is not recommended as settings should be explicitly provided. > test-validate.R: i NOTE that this can cause problems with settings. > test-validate.R: v The is suppressed with minCellCount = 2. [ FAIL 0 | WARN 0 | SKIP 3 | PASS 1413 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • On CRAN (3): 'test-assert.R:344:3', 'test-logger.R:41:3', 'test-utilities.R:212:1' [ FAIL 0 | WARN 0 | SKIP 3 | PASS 1413 ] > > proc.time() user system elapsed 3.20 0.32 35.90