• using R Under development (unstable) (2024-05-21 r86571)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 18.1.5     flang-new version 18.1.5
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• 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 whether package ‘CohortCharacteristics’ can be installed ... [14s/16s] OK See the install log for details.
• checking installed package size ... NOTE   installed size is 6.2Mb   sub-directories of 1Mb or more:     doc 5.6Mb
• 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 ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... NOTE Namespaces in Imports field not imported from:   ‘lifecycle’ ‘lubridate’   All declared Imports should be used.
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [28s/31s] OK
• checking Rd files ... 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 ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [201s/126s] ERROR   Running ‘spelling.R’   Running ‘testthat.R’ [200s/125s] 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 ... [227s/237s] 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: /data/gannet/ripley/R/packages/tests-clang/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: /data/gannet/ripley/R/packages/tests-clang/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: /data/gannet/ripley/R/packages/tests-clang/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: /data/gannet/ripley/R/packages/tests-clang/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 = 46351 bytes Input file size = 47269 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 (5066 bytes decrease) Output file size = 41363 bytes (5906 bytes = 12.49% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/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 ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs, 1 WARNING, 2 NOTEs