* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortCharacteristics.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (Debian 13.2.0-24) 13.2.0 GNU Fortran (Debian 13.2.0-24) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘CohortCharacteristics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CohortCharacteristics’ version ‘0.2.0’ * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘CohortCharacteristics’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/CohortCharacteristics-00install.html' for details. * checking package directory ... OK * checking for future file timestamps ... 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/2s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/2s] OK * checking loading without being on the library search path ... [1s/2s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [20s/28s] OK * checking Rd files ... [1s/1s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'mockCohortCharacteristics.Rd': mockCohortCharacteristics Code: function(con = NULL, writeSchema = NULL, numberIndividuals = 10, ..., seed = NULL) Docs: function(connectionDetails = list(con = DBI::dbConnect(duckdb::duckdb(), ":memory:"), write_schema = "main", mock_prefix = NULL), drug_exposure = NULL, drug_strength = NULL, observation_period = NULL, condition_occurrence = NULL, visit_occurrence = NULL, concept_ancestor = NULL, person = NULL, death = NULL, cohort1 = NULL, cohort2 = NULL, drug_concept_id_size = 5, ancestor_concept_id_size = 5, condition_concept_id_size = 5, visit_concept_id_size = 5, visit_occurrence_id_size = 5, ingredient_concept_id_size = 1, drug_exposure_size = 10, patient_size = 1, min_drug_exposure_start_date = "2000-01-01", max_drug_exposure_start_date = "2020-01-01", earliest_date_of_birth = NULL, latest_date_of_birth = NULL, earliest_observation_start_date = NULL, latest_observation_start_date = NULL, min_days_to_observation_end = NULL, max_days_to_observation_end = NULL, earliest_condition_start_date = NULL, latest_condition_start_date = NULL, min_days_to_condition_end = NULL, max_days_to_condition_end = NULL, earliest_visit_start_date = NULL, latest_visit_start_date = NULL, min_days_to_visit_end = NULL, max_days_to_visit_end = NULL, seed = 1, ...) Argument names in code not in docs: con writeSchema numberIndividuals Argument names in docs not in code: connectionDetails drug_exposure drug_strength observation_period condition_occurrence visit_occurrence concept_ancestor person death cohort1 cohort2 drug_concept_id_size ancestor_concept_id_size condition_concept_id_size visit_concept_id_size visit_occurrence_id_size ingredient_concept_id_size drug_exposure_size patient_size min_drug_exposure_start_date max_drug_exposure_start_date earliest_date_of_birth latest_date_of_birth earliest_observation_start_date latest_observation_start_date min_days_to_observation_end max_days_to_observation_end earliest_condition_start_date latest_condition_start_date min_days_to_condition_end max_days_to_condition_end earliest_visit_start_date latest_visit_start_date min_days_to_visit_end max_days_to_visit_end Mismatches in argument names (first 3): Position: 1 Code: con Docs: connectionDetails Position: 2 Code: writeSchema Docs: drug_exposure Position: 3 Code: numberIndividuals Docs: drug_strength Mismatches in argument default values: Name: 'seed' Code: NULL Docs: 1 * 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 ... [2s/2s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [164s/128s] ERROR Running ‘spelling.R’ [0s/1s] Running ‘testthat.R’ [163s/127s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(CohortCharacteristics) > > test_check("CohortCharacteristics") Starting 2 test processes [ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ] ══ Skipped tests (11) ══════════════════════════════════════════════════════════ • On CRAN (10): 'test-plotCharacteristics.R:2:3', 'test-plotLargeScaleCharacteristics.R:3:3', 'test-plotSummarised.R:2:3', 'test-plotSummarised.R:91:3', 'test-plotSummarised.R:197:3', 'test-plotSummarised.R:299:3', 'test-summariseLargeScaleCharacteristics.R:2:3', 'test-tableSummarised.R:2:3', 'test-tableSummarised.R:123:3', 'test-summariseCharacteristics.R:1122:3' • empty test (1): 'test-tableSummarised.R:262:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-summariseCharacteristics.R:53:3'): test summariseCharacteristics ── Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort, person = person, comorbidities = comorbidities, medication = medication, observation_period = observation_period, cohort1 = emptyCohort, cohort2 = emptyCohort)`: ! `con` must be a DBI connection Backtrace: ▆ 1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:53:3 2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection")) 3. └─rlang::abort(...) ── Error ('test-summariseCharacteristics.R:378:3'): test empty cohort ────────── Error in `mockCohortCharacteristics(connectionDetails = connectionDetails)`: tables must be a list; it can not contain NA; it can not be NULL; it has to be named; elements must have class: data.frame. Backtrace: ▆ 1. └─PatientProfiles (local) mockCohortCharacteristics(connectionDetails = connectionDetails) at test-summariseCharacteristics.R:378:3 2. └─PatientProfiles:::assertList(tables, named = TRUE, class = "data.frame") 3. └─cli::cli_abort(errorMessage, call = call) 4. └─rlang::abort(...) ── Error ('test-summariseCharacteristics.R:484:3'): test cohort id ───────────── Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort, person = person, comorbidities = comorbidities, medication = medication, observation_period = observation_period, cohort1 = emptyCohort, cohort2 = emptyCohort)`: ! `con` must be a DBI connection Backtrace: ▆ 1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:484:3 2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection")) 3. └─rlang::abort(...) [ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [186s/239s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘a05_summariseCohortEntries.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a05_summariseCohortEntries.Rmd’ Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. --- re-building ‘a06_summarisePatientCharacteristics.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Quitting from lines 78-86 [unnamed-chunk-5] (a06_summarisePatientCharacteristics.Rmd) Error: processing vignette 'a06_summarisePatientCharacteristics.Rmd' failed with diagnostics: the condition has length > 1 --- failed re-building ‘a06_summarisePatientCharacteristics.Rmd’ Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. --- re-building ‘a07_summariseLargeScaleCharacteristics.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a07_summariseLargeScaleCharacteristics.Rmd’ Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. --- re-building ‘a08_summariseCohortOverlap.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a08_summariseCohortOverlap_files/figure-html/unnamed-chunk-5-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 37316 bytes Input file size = 37442 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33427 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 32928 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 32928 Output IDAT size = 32928 bytes (4388 bytes decrease) Output file size = 33006 bytes (4436 bytes = 11.85% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a08_summariseCohortOverlap_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 66151 bytes Input file size = 66325 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53846 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53846 Output IDAT size = 53846 bytes (12305 bytes decrease) Output file size = 53924 bytes (12401 bytes = 18.70% decrease) --- finished re-building ‘a08_summariseCohortOverlap.Rmd’ Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. --- re-building ‘a09_summariseCohortTiming.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-5-1.png 1344x960 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 17931 bytes Input file size = 18810 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14167 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 11762 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11690 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11690 Output IDAT size = 11690 bytes (6241 bytes decrease) Output file size = 11768 bytes (7042 bytes = 37.44% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-6-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 46347 bytes Input file size = 47265 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41285 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41285 Output IDAT size = 41285 bytes (5062 bytes decrease) Output file size = 41363 bytes (5902 bytes = 12.49% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-7-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 64596 bytes Input file size = 64758 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56755 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56755 Output IDAT size = 56755 bytes (7841 bytes decrease) Output file size = 56833 bytes (7925 bytes = 12.24% decrease) --- finished re-building ‘a09_summariseCohortTiming.Rmd’ Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. SUMMARY: processing the following file failed: ‘a06_summarisePatientCharacteristics.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [6s/8s] OK * checking HTML version of manual ... [1s/2s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 2 ERRORs, 1 WARNING