CRAN Package Check Results for Package DrugUtilisation

Last updated on 2024-12-06 22:49:59 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.7.1 8.38 497.12 505.50 ERROR
r-devel-linux-x86_64-debian-gcc 0.7.1 4.61 361.72 366.33 ERROR
r-devel-linux-x86_64-fedora-clang 0.7.1 793.82 ERROR
r-devel-linux-x86_64-fedora-gcc 0.7.1 760.48 ERROR
r-devel-windows-x86_64 0.7.1 9.00 306.00 315.00 ERROR
r-patched-linux-x86_64 0.7.1 10.13 468.99 479.12 ERROR
r-release-linux-x86_64 0.7.1 8.82 481.37 490.19 OK
r-release-macos-arm64 0.7.1 166.00 OK
r-release-macos-x86_64 0.7.1 314.00 OK
r-release-windows-x86_64 0.7.1 11.00 333.00 344.00 ERROR
r-oldrel-macos-arm64 0.7.1 129.00 OK
r-oldrel-macos-x86_64 0.7.1 271.00 OK
r-oldrel-windows-x86_64 0.7.1 13.00 434.00 447.00 ERROR

Check Details

Version: 0.7.1
Check: dependencies in R code
Result: WARN Missing or unexported object: ‘visOmopResults::optionsVisOmopTable’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 0.7.1
Check: examples
Result: ERROR Running examples in ‘DrugUtilisation-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: defaultTableOptions > ### Title: Additional arguments for the table functions. > ### Aliases: defaultTableOptions > > ### ** Examples > > { + defaultTableOptions() + } Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

Version: 0.7.1
Check: tests
Result: ERROR Running ‘testthat.R’ [282s/161s] 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(DrugUtilisation) > > test_check("DrugUtilisation") Starting 2 test processes [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] ══ Skipped tests (50) ══════════════════════════════════════════════════════════ • On CRAN (50): 'test-benchmarkDrugUtilisation.R:2:3', 'test-addDrugUtilisation.R:3:3', 'test-addDrugUtilisation.R:156:3', 'test-addDrugUtilisation.R:196:3', 'test-dailyDose.R:2:3', 'test-generateDrugUtilisationCohortSet.R:2:3', 'test-generateDrugUtilisationCohortSet.R:23:3', 'test-generatedAtcCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:39:3', 'test-generatedIngredientCohortSet.R:54:3', 'test-generatedIngredientCohortSet.R:69:3', 'test-generatedIngredientCohortSet.R:98:3', 'test-drugUse.R:2:3', 'test-drugUse.R:42:3', 'test-drugUse.R:259:3', 'test-drugUse.R:463:3', 'test-drugUse.R:608:3', 'test-drugUse.R:860:3', 'test-drugUse.R:883:3', 'test-drugUse.R:932:3', 'test-drugUse.R:967:3', 'test-drugUse.R:1025:3', 'test-patterns.R:2:3', 'test-plotProportionOfPatientsCovered.R:2:3', 'test-plotProportionOfPatientsCovered.R:58:3', 'test-plotProportionOfPatientsCovered.R:100:3', 'test-plotTreatment.R:2:3', 'test-plots.R:2:3', 'test-readConceptList.R:2:3', 'test-require.R:2:3', 'test-require.R:143:3', 'test-require.R:324:3', 'test-require.R:432:3', 'test-require.R:526:3', 'test-require.R:597:3', 'test-indication.R:2:3', 'test-indication.R:202:3', 'test-indication.R:364:3', 'test-indication.R:481:3', 'test-summariseProportionOfPatientsCovered.R:94:3', 'test-summariseProportionOfPatientsCovered.R:170:3', 'test-summariseProportionOfPatientsCovered.R:277:3', 'test-summariseProportionOfPatientsCovered.R:497:3', 'test-summariseProportionOfPatientsCovered.R:550:3', 'test-tables.R:2:3', 'test-tables.R:132:3', 'test-tables.R:271:3', 'test-tables.R:393:3', 'test-tables.R:502:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-summariseDrugRestart.R:76:3'): summarise drug restart ──────── is.na(settings(resultsCohort)$censor_date) is not TRUE `actual`: `expected`: TRUE ── Failure ('test-summariseDrugRestart.R:83:3'): summarise drug restart ──────── unique(resultsSup$estimate_value) (`actual`) not equal to c(NA_character_, "0") (`expected`). `actual`: "-" "0" `expected`: NA "0" ── Failure ('test-summariseTreatment.R:49:3'): test summariseTreatment ───────── all(...) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-summariseDrugUtilisation.R:65:3'): summariseDrugUtilisation works ── all(...) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.7.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘create_cohorts.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-9-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24762 bytes Input file size = 24876 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20566 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 = 20566 Output IDAT size = 20566 bytes (4196 bytes decrease) Output file size = 20644 bytes (4232 bytes = 17.01% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-10-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3638 bytes Input file size = 4364 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3050 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3032 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 = 1 f = 0 IDAT size = 3032 Output IDAT size = 3032 bytes (606 bytes decrease) Output file size = 3758 bytes (606 bytes = 13.89% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-11-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3617 bytes Input file size = 4343 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3032 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3011 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 = 1 f = 0 IDAT size = 3011 Output IDAT size = 3011 bytes (606 bytes decrease) Output file size = 3737 bytes (606 bytes = 13.95% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-12-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3563 bytes Input file size = 4289 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2989 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2969 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 = 1 f = 0 IDAT size = 2969 Output IDAT size = 2969 bytes (594 bytes decrease) Output file size = 3695 bytes (594 bytes = 13.85% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-42-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11056 bytes Input file size = 11146 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8629 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 = 8629 Output IDAT size = 8629 bytes (2427 bytes decrease) Output file size = 8707 bytes (2439 bytes = 21.88% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-43-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7942 bytes Input file size = 8020 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6505 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 = 6505 Output IDAT size = 6505 bytes (1437 bytes decrease) Output file size = 6583 bytes (1437 bytes = 17.92% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-44-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7940 bytes Input file size = 8018 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6533 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 = 6533 Output IDAT size = 6533 bytes (1407 bytes decrease) Output file size = 6611 bytes (1407 bytes = 17.55% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-45-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7777 bytes Input file size = 7855 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6351 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 = 6351 Output IDAT size = 6351 bytes (1426 bytes decrease) Output file size = 6429 bytes (1426 bytes = 18.15% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-46-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7789 bytes Input file size = 7867 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6381 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 = 6381 Output IDAT size = 6381 bytes (1408 bytes decrease) Output file size = 6459 bytes (1408 bytes = 17.90% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-47-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7432 bytes Input file size = 7510 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6162 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 = 6162 Output IDAT size = 6162 bytes (1270 bytes decrease) Output file size = 6240 bytes (1270 bytes = 16.91% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-48-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7445 bytes Input file size = 7523 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6182 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 = 6182 Output IDAT size = 6182 bytes (1263 bytes decrease) Output file size = 6260 bytes (1263 bytes = 16.79% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-49-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7940 bytes Input file size = 8018 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6533 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 = 6533 Output IDAT size = 6533 bytes (1407 bytes decrease) Output file size = 6611 bytes (1407 bytes = 17.55% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-50-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8705 bytes Input file size = 8795 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7098 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 = 7098 Output IDAT size = 7098 bytes (1607 bytes decrease) Output file size = 7176 bytes (1619 bytes = 18.41% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-51-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8332 bytes Input file size = 8422 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6889 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 = 6889 Output IDAT size = 6889 bytes (1443 bytes decrease) Output file size = 6967 bytes (1455 bytes = 17.28% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-52-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8356 bytes Input file size = 8446 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6922 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 = 6922 Output IDAT size = 6922 bytes (1434 bytes decrease) Output file size = 7000 bytes (1446 bytes = 17.12% decrease) --- finished re-building ‘create_cohorts.Rmd’ --- re-building ‘drug_utilisation.Rmd’ using rmarkdown Quitting from lines 277-278 [unnamed-chunk-9] (drug_utilisation.Rmd) Error: processing vignette 'drug_utilisation.Rmd' failed with diagnostics: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' --- failed re-building ‘drug_utilisation.Rmd’ SUMMARY: processing the following file failed: ‘drug_utilisation.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.7.1
Check: tests
Result: ERROR Running ‘testthat.R’ [209s/164s] 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(DrugUtilisation) > > test_check("DrugUtilisation") Starting 2 test processes [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] ══ Skipped tests (50) ══════════════════════════════════════════════════════════ • On CRAN (50): 'test-addDrugUtilisation.R:3:3', 'test-addDrugUtilisation.R:156:3', 'test-addDrugUtilisation.R:196:3', 'test-benchmarkDrugUtilisation.R:2:3', 'test-dailyDose.R:2:3', 'test-generateDrugUtilisationCohortSet.R:2:3', 'test-generateDrugUtilisationCohortSet.R:23:3', 'test-generatedAtcCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:39:3', 'test-generatedIngredientCohortSet.R:54:3', 'test-generatedIngredientCohortSet.R:69:3', 'test-generatedIngredientCohortSet.R:98:3', 'test-drugUse.R:2:3', 'test-drugUse.R:42:3', 'test-drugUse.R:259:3', 'test-drugUse.R:463:3', 'test-drugUse.R:608:3', 'test-drugUse.R:860:3', 'test-drugUse.R:883:3', 'test-drugUse.R:932:3', 'test-drugUse.R:967:3', 'test-drugUse.R:1025:3', 'test-patterns.R:2:3', 'test-plotProportionOfPatientsCovered.R:2:3', 'test-plotProportionOfPatientsCovered.R:58:3', 'test-plotProportionOfPatientsCovered.R:100:3', 'test-plotTreatment.R:2:3', 'test-plots.R:2:3', 'test-readConceptList.R:2:3', 'test-require.R:2:3', 'test-require.R:143:3', 'test-require.R:324:3', 'test-require.R:432:3', 'test-require.R:526:3', 'test-require.R:597:3', 'test-indication.R:2:3', 'test-indication.R:202:3', 'test-indication.R:364:3', 'test-indication.R:481:3', 'test-summariseProportionOfPatientsCovered.R:94:3', 'test-summariseProportionOfPatientsCovered.R:170:3', 'test-summariseProportionOfPatientsCovered.R:277:3', 'test-summariseProportionOfPatientsCovered.R:497:3', 'test-summariseProportionOfPatientsCovered.R:550:3', 'test-tables.R:2:3', 'test-tables.R:132:3', 'test-tables.R:271:3', 'test-tables.R:393:3', 'test-tables.R:502:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-summariseDrugRestart.R:76:3'): summarise drug restart ──────── is.na(settings(resultsCohort)$censor_date) is not TRUE `actual`: `expected`: TRUE ── Failure ('test-summariseDrugRestart.R:83:3'): summarise drug restart ──────── unique(resultsSup$estimate_value) (`actual`) not equal to c(NA_character_, "0") (`expected`). `actual`: "-" "0" `expected`: NA "0" ── Failure ('test-summariseTreatment.R:49:3'): test summariseTreatment ───────── all(...) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-summariseDrugUtilisation.R:65:3'): summariseDrugUtilisation works ── all(...) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.7.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘create_cohorts.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-9-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24762 bytes Input file size = 24876 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20566 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 = 20566 Output IDAT size = 20566 bytes (4196 bytes decrease) Output file size = 20644 bytes (4232 bytes = 17.01% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-10-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3638 bytes Input file size = 4364 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3050 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3032 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 = 1 f = 0 IDAT size = 3032 Output IDAT size = 3032 bytes (606 bytes decrease) Output file size = 3758 bytes (606 bytes = 13.89% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-11-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3617 bytes Input file size = 4343 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3032 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3011 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 = 1 f = 0 IDAT size = 3011 Output IDAT size = 3011 bytes (606 bytes decrease) Output file size = 3737 bytes (606 bytes = 13.95% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-12-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3563 bytes Input file size = 4289 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2989 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2969 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 = 1 f = 0 IDAT size = 2969 Output IDAT size = 2969 bytes (594 bytes decrease) Output file size = 3695 bytes (594 bytes = 13.85% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-42-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11056 bytes Input file size = 11146 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8629 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 = 8629 Output IDAT size = 8629 bytes (2427 bytes decrease) Output file size = 8707 bytes (2439 bytes = 21.88% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-43-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7942 bytes Input file size = 8020 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6505 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 = 6505 Output IDAT size = 6505 bytes (1437 bytes decrease) Output file size = 6583 bytes (1437 bytes = 17.92% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-44-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7940 bytes Input file size = 8018 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6533 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 = 6533 Output IDAT size = 6533 bytes (1407 bytes decrease) Output file size = 6611 bytes (1407 bytes = 17.55% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-45-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7777 bytes Input file size = 7855 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6351 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 = 6351 Output IDAT size = 6351 bytes (1426 bytes decrease) Output file size = 6429 bytes (1426 bytes = 18.15% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-46-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7789 bytes Input file size = 7867 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6381 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 = 6381 Output IDAT size = 6381 bytes (1408 bytes decrease) Output file size = 6459 bytes (1408 bytes = 17.90% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-47-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7432 bytes Input file size = 7510 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6162 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 = 6162 Output IDAT size = 6162 bytes (1270 bytes decrease) Output file size = 6240 bytes (1270 bytes = 16.91% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-48-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7445 bytes Input file size = 7523 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6182 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 = 6182 Output IDAT size = 6182 bytes (1263 bytes decrease) Output file size = 6260 bytes (1263 bytes = 16.79% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-49-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7940 bytes Input file size = 8018 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6533 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 = 6533 Output IDAT size = 6533 bytes (1407 bytes decrease) Output file size = 6611 bytes (1407 bytes = 17.55% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-50-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8705 bytes Input file size = 8795 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7098 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 = 7098 Output IDAT size = 7098 bytes (1607 bytes decrease) Output file size = 7176 bytes (1619 bytes = 18.41% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-51-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8332 bytes Input file size = 8422 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6889 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 = 6889 Output IDAT size = 6889 bytes (1443 bytes decrease) Output file size = 6967 bytes (1455 bytes = 17.28% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-52-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8356 bytes Input file size = 8446 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6922 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 = 6922 Output IDAT size = 6922 bytes (1434 bytes decrease) Output file size = 7000 bytes (1446 bytes = 17.12% decrease) --- finished re-building ‘create_cohorts.Rmd’ --- re-building ‘drug_utilisation.Rmd’ using rmarkdown Quitting from lines 277-278 [unnamed-chunk-9] (drug_utilisation.Rmd) Error: processing vignette 'drug_utilisation.Rmd' failed with diagnostics: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' --- failed re-building ‘drug_utilisation.Rmd’ SUMMARY: processing the following file failed: ‘drug_utilisation.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.7.1
Check: examples
Result: ERROR Running examples in ‘DrugUtilisation-Ex.R’ failed The error most likely occurred in: > ### Name: defaultTableOptions > ### Title: Additional arguments for the table functions. > ### Aliases: defaultTableOptions > > ### ** Examples > > { + defaultTableOptions() + } Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 0.7.1
Check: tests
Result: ERROR Running ‘testthat.R’ [436s/251s] 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(DrugUtilisation) > > test_check("DrugUtilisation") Starting 2 test processes [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] ══ Skipped tests (50) ══════════════════════════════════════════════════════════ • On CRAN (50): 'test-benchmarkDrugUtilisation.R:2:3', 'test-addDrugUtilisation.R:3:3', 'test-addDrugUtilisation.R:156:3', 'test-addDrugUtilisation.R:196:3', 'test-dailyDose.R:2:3', 'test-generateDrugUtilisationCohortSet.R:2:3', 'test-generateDrugUtilisationCohortSet.R:23:3', 'test-generatedAtcCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:39:3', 'test-generatedIngredientCohortSet.R:54:3', 'test-generatedIngredientCohortSet.R:69:3', 'test-generatedIngredientCohortSet.R:98:3', 'test-drugUse.R:2:3', 'test-drugUse.R:42:3', 'test-drugUse.R:259:3', 'test-drugUse.R:463:3', 'test-drugUse.R:608:3', 'test-drugUse.R:860:3', 'test-drugUse.R:883:3', 'test-drugUse.R:932:3', 'test-drugUse.R:967:3', 'test-drugUse.R:1025:3', 'test-patterns.R:2:3', 'test-plotProportionOfPatientsCovered.R:2:3', 'test-plotProportionOfPatientsCovered.R:58:3', 'test-plotProportionOfPatientsCovered.R:100:3', 'test-plotTreatment.R:2:3', 'test-plots.R:2:3', 'test-readConceptList.R:2:3', 'test-require.R:2:3', 'test-require.R:143:3', 'test-require.R:324:3', 'test-require.R:432:3', 'test-require.R:526:3', 'test-require.R:597:3', 'test-indication.R:2:3', 'test-indication.R:202:3', 'test-indication.R:364:3', 'test-indication.R:481:3', 'test-summariseProportionOfPatientsCovered.R:94:3', 'test-summariseProportionOfPatientsCovered.R:170:3', 'test-summariseProportionOfPatientsCovered.R:277:3', 'test-summariseProportionOfPatientsCovered.R:497:3', 'test-summariseProportionOfPatientsCovered.R:550:3', 'test-tables.R:2:3', 'test-tables.R:132:3', 'test-tables.R:271:3', 'test-tables.R:393:3', 'test-tables.R:502:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-summariseDrugRestart.R:76:3'): summarise drug restart ──────── is.na(settings(resultsCohort)$censor_date) is not TRUE `actual`: `expected`: TRUE ── Failure ('test-summariseDrugRestart.R:83:3'): summarise drug restart ──────── unique(resultsSup$estimate_value) (`actual`) not equal to c(NA_character_, "0") (`expected`). `actual`: "-" "0" `expected`: NA "0" ── Failure ('test-summariseTreatment.R:49:3'): test summariseTreatment ───────── all(...) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-summariseDrugUtilisation.R:65:3'): summariseDrugUtilisation works ── all(...) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.7.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘create_cohorts.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-9-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24767 bytes Input file size = 24881 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20565 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 = 20565 Output IDAT size = 20565 bytes (4202 bytes decrease) Output file size = 20643 bytes (4238 bytes = 17.03% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-10-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3638 bytes Input file size = 4364 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3050 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3032 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 = 1 f = 0 IDAT size = 3032 Output IDAT size = 3032 bytes (606 bytes decrease) Output file size = 3758 bytes (606 bytes = 13.89% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-11-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3617 bytes Input file size = 4343 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3032 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3011 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 = 1 f = 0 IDAT size = 3011 Output IDAT size = 3011 bytes (606 bytes decrease) Output file size = 3737 bytes (606 bytes = 13.95% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-12-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3563 bytes Input file size = 4289 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2989 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2969 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 = 1 f = 0 IDAT size = 2969 Output IDAT size = 2969 bytes (594 bytes decrease) Output file size = 3695 bytes (594 bytes = 13.85% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-42-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11056 bytes Input file size = 11146 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8629 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 = 8629 Output IDAT size = 8629 bytes (2427 bytes decrease) Output file size = 8707 bytes (2439 bytes = 21.88% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-43-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7942 bytes Input file size = 8020 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6505 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 = 6505 Output IDAT size = 6505 bytes (1437 bytes decrease) Output file size = 6583 bytes (1437 bytes = 17.92% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-44-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7940 bytes Input file size = 8018 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6533 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 = 6533 Output IDAT size = 6533 bytes (1407 bytes decrease) Output file size = 6611 bytes (1407 bytes = 17.55% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-45-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7777 bytes Input file size = 7855 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6351 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 = 6351 Output IDAT size = 6351 bytes (1426 bytes decrease) Output file size = 6429 bytes (1426 bytes = 18.15% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-46-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7789 bytes Input file size = 7867 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6381 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 = 6381 Output IDAT size = 6381 bytes (1408 bytes decrease) Output file size = 6459 bytes (1408 bytes = 17.90% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-47-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7432 bytes Input file size = 7510 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6162 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 = 6162 Output IDAT size = 6162 bytes (1270 bytes decrease) Output file size = 6240 bytes (1270 bytes = 16.91% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-48-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7445 bytes Input file size = 7523 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6182 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 = 6182 Output IDAT size = 6182 bytes (1263 bytes decrease) Output file size = 6260 bytes (1263 bytes = 16.79% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-49-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7940 bytes Input file size = 8018 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6533 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 = 6533 Output IDAT size = 6533 bytes (1407 bytes decrease) Output file size = 6611 bytes (1407 bytes = 17.55% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-50-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8705 bytes Input file size = 8795 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7098 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 = 7098 Output IDAT size = 7098 bytes (1607 bytes decrease) Output file size = 7176 bytes (1619 bytes = 18.41% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-51-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8332 bytes Input file size = 8422 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6889 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 = 6889 Output IDAT size = 6889 bytes (1443 bytes decrease) Output file size = 6967 bytes (1455 bytes = 17.28% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-52-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8356 bytes Input file size = 8446 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6922 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 = 6922 Output IDAT size = 6922 bytes (1434 bytes decrease) Output file size = 7000 bytes (1446 bytes = 17.12% decrease) --- finished re-building ‘create_cohorts.Rmd’ --- re-building ‘drug_utilisation.Rmd’ using rmarkdown Quitting from lines 277-278 [unnamed-chunk-9] (drug_utilisation.Rmd) Error: processing vignette 'drug_utilisation.Rmd' failed with diagnostics: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' --- failed re-building ‘drug_utilisation.Rmd’ SUMMARY: processing the following file failed: ‘drug_utilisation.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.7.1
Check: tests
Result: ERROR Running ‘testthat.R’ [413s/232s] 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(DrugUtilisation) > > test_check("DrugUtilisation") Starting 2 test processes [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] ══ Skipped tests (50) ══════════════════════════════════════════════════════════ • On CRAN (50): 'test-benchmarkDrugUtilisation.R:2:3', 'test-addDrugUtilisation.R:3:3', 'test-addDrugUtilisation.R:156:3', 'test-addDrugUtilisation.R:196:3', 'test-dailyDose.R:2:3', 'test-generateDrugUtilisationCohortSet.R:2:3', 'test-generateDrugUtilisationCohortSet.R:23:3', 'test-generatedAtcCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:39:3', 'test-generatedIngredientCohortSet.R:54:3', 'test-generatedIngredientCohortSet.R:69:3', 'test-generatedIngredientCohortSet.R:98:3', 'test-drugUse.R:2:3', 'test-drugUse.R:42:3', 'test-drugUse.R:259:3', 'test-drugUse.R:463:3', 'test-drugUse.R:608:3', 'test-drugUse.R:860:3', 'test-drugUse.R:883:3', 'test-drugUse.R:932:3', 'test-drugUse.R:967:3', 'test-drugUse.R:1025:3', 'test-patterns.R:2:3', 'test-plotProportionOfPatientsCovered.R:2:3', 'test-plotProportionOfPatientsCovered.R:58:3', 'test-plotProportionOfPatientsCovered.R:100:3', 'test-plotTreatment.R:2:3', 'test-plots.R:2:3', 'test-readConceptList.R:2:3', 'test-require.R:2:3', 'test-require.R:143:3', 'test-require.R:324:3', 'test-require.R:432:3', 'test-require.R:526:3', 'test-require.R:597:3', 'test-indication.R:2:3', 'test-indication.R:202:3', 'test-indication.R:364:3', 'test-indication.R:481:3', 'test-summariseProportionOfPatientsCovered.R:94:3', 'test-summariseProportionOfPatientsCovered.R:170:3', 'test-summariseProportionOfPatientsCovered.R:277:3', 'test-summariseProportionOfPatientsCovered.R:497:3', 'test-summariseProportionOfPatientsCovered.R:550:3', 'test-tables.R:2:3', 'test-tables.R:132:3', 'test-tables.R:271:3', 'test-tables.R:393:3', 'test-tables.R:502:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-summariseDrugRestart.R:76:3'): summarise drug restart ──────── is.na(settings(resultsCohort)$censor_date) is not TRUE `actual`: `expected`: TRUE ── Failure ('test-summariseDrugRestart.R:83:3'): summarise drug restart ──────── unique(resultsSup$estimate_value) (`actual`) not equal to c(NA_character_, "0") (`expected`). `actual`: "-" "0" `expected`: NA "0" ── Failure ('test-summariseTreatment.R:49:3'): test summariseTreatment ───────── all(...) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-summariseDrugUtilisation.R:65:3'): summariseDrugUtilisation works ── all(...) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.7.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘create_cohorts.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-9-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24767 bytes Input file size = 24881 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20565 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 = 20565 Output IDAT size = 20565 bytes (4202 bytes decrease) Output file size = 20643 bytes (4238 bytes = 17.03% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-10-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3638 bytes Input file size = 4364 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3050 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3032 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 = 1 f = 0 IDAT size = 3032 Output IDAT size = 3032 bytes (606 bytes decrease) Output file size = 3758 bytes (606 bytes = 13.89% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-11-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3617 bytes Input file size = 4343 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3032 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3011 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 = 1 f = 0 IDAT size = 3011 Output IDAT size = 3011 bytes (606 bytes decrease) Output file size = 3737 bytes (606 bytes = 13.95% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-12-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3563 bytes Input file size = 4289 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2989 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2969 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 = 1 f = 0 IDAT size = 2969 Output IDAT size = 2969 bytes (594 bytes decrease) Output file size = 3695 bytes (594 bytes = 13.85% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-42-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11056 bytes Input file size = 11146 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8629 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 = 8629 Output IDAT size = 8629 bytes (2427 bytes decrease) Output file size = 8707 bytes (2439 bytes = 21.88% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-43-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7942 bytes Input file size = 8020 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6505 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 = 6505 Output IDAT size = 6505 bytes (1437 bytes decrease) Output file size = 6583 bytes (1437 bytes = 17.92% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-44-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7940 bytes Input file size = 8018 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6533 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 = 6533 Output IDAT size = 6533 bytes (1407 bytes decrease) Output file size = 6611 bytes (1407 bytes = 17.55% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-45-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7777 bytes Input file size = 7855 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6351 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 = 6351 Output IDAT size = 6351 bytes (1426 bytes decrease) Output file size = 6429 bytes (1426 bytes = 18.15% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-46-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7789 bytes Input file size = 7867 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6381 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 = 6381 Output IDAT size = 6381 bytes (1408 bytes decrease) Output file size = 6459 bytes (1408 bytes = 17.90% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-47-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7432 bytes Input file size = 7510 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6162 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 = 6162 Output IDAT size = 6162 bytes (1270 bytes decrease) Output file size = 6240 bytes (1270 bytes = 16.91% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-48-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7445 bytes Input file size = 7523 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6182 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 = 6182 Output IDAT size = 6182 bytes (1263 bytes decrease) Output file size = 6260 bytes (1263 bytes = 16.79% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-49-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7940 bytes Input file size = 8018 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6533 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 = 6533 Output IDAT size = 6533 bytes (1407 bytes decrease) Output file size = 6611 bytes (1407 bytes = 17.55% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-50-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8705 bytes Input file size = 8795 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7098 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 = 7098 Output IDAT size = 7098 bytes (1607 bytes decrease) Output file size = 7176 bytes (1619 bytes = 18.41% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-51-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8332 bytes Input file size = 8422 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6889 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 = 6889 Output IDAT size = 6889 bytes (1443 bytes decrease) Output file size = 6967 bytes (1455 bytes = 17.28% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-52-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8356 bytes Input file size = 8446 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6922 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 = 6922 Output IDAT size = 6922 bytes (1434 bytes decrease) Output file size = 7000 bytes (1446 bytes = 17.12% decrease) --- finished re-building ‘create_cohorts.Rmd’ --- re-building ‘drug_utilisation.Rmd’ using rmarkdown Quitting from lines 277-278 [unnamed-chunk-9] (drug_utilisation.Rmd) Error: processing vignette 'drug_utilisation.Rmd' failed with diagnostics: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' --- failed re-building ‘drug_utilisation.Rmd’ SUMMARY: processing the following file failed: ‘drug_utilisation.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.7.1
Check: tests
Result: ERROR Running 'testthat.R' [117s] 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(DrugUtilisation) > > test_check("DrugUtilisation") Starting 2 test processes [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] ══ Skipped tests (50) ══════════════════════════════════════════════════════════ • On CRAN (50): 'test-addDrugUtilisation.R:3:3', 'test-addDrugUtilisation.R:156:3', 'test-addDrugUtilisation.R:196:3', 'test-benchmarkDrugUtilisation.R:2:3', 'test-dailyDose.R:2:3', 'test-generateDrugUtilisationCohortSet.R:2:3', 'test-generateDrugUtilisationCohortSet.R:23:3', 'test-generatedAtcCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:39:3', 'test-generatedIngredientCohortSet.R:54:3', 'test-generatedIngredientCohortSet.R:69:3', 'test-generatedIngredientCohortSet.R:98:3', 'test-drugUse.R:2:3', 'test-drugUse.R:42:3', 'test-drugUse.R:259:3', 'test-drugUse.R:463:3', 'test-drugUse.R:608:3', 'test-drugUse.R:860:3', 'test-drugUse.R:883:3', 'test-drugUse.R:932:3', 'test-drugUse.R:967:3', 'test-drugUse.R:1025:3', 'test-patterns.R:2:3', 'test-plotProportionOfPatientsCovered.R:2:3', 'test-plotProportionOfPatientsCovered.R:58:3', 'test-plotProportionOfPatientsCovered.R:100:3', 'test-plotTreatment.R:2:3', 'test-plots.R:2:3', 'test-readConceptList.R:2:3', 'test-require.R:2:3', 'test-require.R:143:3', 'test-require.R:324:3', 'test-require.R:432:3', 'test-require.R:526:3', 'test-require.R:597:3', 'test-indication.R:2:3', 'test-indication.R:202:3', 'test-indication.R:364:3', 'test-indication.R:481:3', 'test-summariseProportionOfPatientsCovered.R:94:3', 'test-summariseProportionOfPatientsCovered.R:170:3', 'test-summariseProportionOfPatientsCovered.R:277:3', 'test-summariseProportionOfPatientsCovered.R:497:3', 'test-summariseProportionOfPatientsCovered.R:550:3', 'test-tables.R:2:3', 'test-tables.R:132:3', 'test-tables.R:271:3', 'test-tables.R:393:3', 'test-tables.R:502:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-summariseDrugRestart.R:76:3'): summarise drug restart ──────── is.na(settings(resultsCohort)$censor_date) is not TRUE `actual`: `expected`: TRUE ── Failure ('test-summariseDrugRestart.R:83:3'): summarise drug restart ──────── unique(resultsSup$estimate_value) (`actual`) not equal to c(NA_character_, "0") (`expected`). `actual`: "-" "0" `expected`: NA "0" ── Failure ('test-summariseTreatment.R:49:3'): test summariseTreatment ───────── all(...) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-summariseDrugUtilisation.R:65:3'): summariseDrugUtilisation works ── all(...) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] Error: Test failures Execution halted Flavor: r-devel-windows-x86_64

Version: 0.7.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'create_cohorts.Rmd' using rmarkdown --- finished re-building 'create_cohorts.Rmd' --- re-building 'drug_utilisation.Rmd' using rmarkdown Quitting from lines 277-278 [unnamed-chunk-9] (drug_utilisation.Rmd) Error: processing vignette 'drug_utilisation.Rmd' failed with diagnostics: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' --- failed re-building 'drug_utilisation.Rmd' SUMMARY: processing the following file failed: 'drug_utilisation.Rmd' Error: Vignette re-building failed. Execution halted Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 0.7.1
Check: tests
Result: ERROR Running ‘testthat.R’ [265s/148s] 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(DrugUtilisation) > > test_check("DrugUtilisation") Starting 2 test processes [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] ══ Skipped tests (50) ══════════════════════════════════════════════════════════ • On CRAN (50): 'test-benchmarkDrugUtilisation.R:2:3', 'test-addDrugUtilisation.R:3:3', 'test-addDrugUtilisation.R:156:3', 'test-addDrugUtilisation.R:196:3', 'test-dailyDose.R:2:3', 'test-generateDrugUtilisationCohortSet.R:2:3', 'test-generateDrugUtilisationCohortSet.R:23:3', 'test-generatedAtcCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:39:3', 'test-generatedIngredientCohortSet.R:54:3', 'test-generatedIngredientCohortSet.R:69:3', 'test-generatedIngredientCohortSet.R:98:3', 'test-drugUse.R:2:3', 'test-drugUse.R:42:3', 'test-drugUse.R:259:3', 'test-drugUse.R:463:3', 'test-drugUse.R:608:3', 'test-drugUse.R:860:3', 'test-drugUse.R:883:3', 'test-drugUse.R:932:3', 'test-drugUse.R:967:3', 'test-drugUse.R:1025:3', 'test-patterns.R:2:3', 'test-plotProportionOfPatientsCovered.R:2:3', 'test-plotProportionOfPatientsCovered.R:58:3', 'test-plotProportionOfPatientsCovered.R:100:3', 'test-plotTreatment.R:2:3', 'test-plots.R:2:3', 'test-readConceptList.R:2:3', 'test-require.R:2:3', 'test-require.R:143:3', 'test-require.R:324:3', 'test-require.R:432:3', 'test-require.R:526:3', 'test-require.R:597:3', 'test-indication.R:2:3', 'test-indication.R:202:3', 'test-indication.R:364:3', 'test-indication.R:481:3', 'test-summariseProportionOfPatientsCovered.R:94:3', 'test-summariseProportionOfPatientsCovered.R:170:3', 'test-summariseProportionOfPatientsCovered.R:277:3', 'test-summariseProportionOfPatientsCovered.R:497:3', 'test-summariseProportionOfPatientsCovered.R:550:3', 'test-tables.R:2:3', 'test-tables.R:132:3', 'test-tables.R:271:3', 'test-tables.R:393:3', 'test-tables.R:502:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-summariseDrugRestart.R:76:3'): summarise drug restart ──────── is.na(settings(resultsCohort)$censor_date) is not TRUE `actual`: `expected`: TRUE ── Failure ('test-summariseDrugRestart.R:83:3'): summarise drug restart ──────── unique(resultsSup$estimate_value) (`actual`) not equal to c(NA_character_, "0") (`expected`). `actual`: "-" "0" `expected`: NA "0" ── Failure ('test-summariseTreatment.R:49:3'): test summariseTreatment ───────── all(...) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-summariseDrugUtilisation.R:65:3'): summariseDrugUtilisation works ── all(...) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] Error: Test failures Execution halted Flavor: r-patched-linux-x86_64

Version: 0.7.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘create_cohorts.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-9-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24762 bytes Input file size = 24876 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20566 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 = 20566 Output IDAT size = 20566 bytes (4196 bytes decrease) Output file size = 20644 bytes (4232 bytes = 17.01% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-10-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3638 bytes Input file size = 4364 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3050 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3032 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 = 1 f = 0 IDAT size = 3032 Output IDAT size = 3032 bytes (606 bytes decrease) Output file size = 3758 bytes (606 bytes = 13.89% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-11-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3617 bytes Input file size = 4343 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3032 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3011 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 = 1 f = 0 IDAT size = 3011 Output IDAT size = 3011 bytes (606 bytes decrease) Output file size = 3737 bytes (606 bytes = 13.95% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-12-1.png 672x192 pixels, 8 bits/pixel, 212 colors in palette Input IDAT size = 3563 bytes Input file size = 4289 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2989 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2969 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 = 1 f = 0 IDAT size = 2969 Output IDAT size = 2969 bytes (594 bytes decrease) Output file size = 3695 bytes (594 bytes = 13.85% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-42-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11056 bytes Input file size = 11146 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8629 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 = 8629 Output IDAT size = 8629 bytes (2427 bytes decrease) Output file size = 8707 bytes (2439 bytes = 21.88% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-43-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7942 bytes Input file size = 8020 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6505 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 = 6505 Output IDAT size = 6505 bytes (1437 bytes decrease) Output file size = 6583 bytes (1437 bytes = 17.92% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-44-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7940 bytes Input file size = 8018 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6533 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 = 6533 Output IDAT size = 6533 bytes (1407 bytes decrease) Output file size = 6611 bytes (1407 bytes = 17.55% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-45-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7777 bytes Input file size = 7855 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6351 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 = 6351 Output IDAT size = 6351 bytes (1426 bytes decrease) Output file size = 6429 bytes (1426 bytes = 18.15% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-46-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7789 bytes Input file size = 7867 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6381 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 = 6381 Output IDAT size = 6381 bytes (1408 bytes decrease) Output file size = 6459 bytes (1408 bytes = 17.90% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-47-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7432 bytes Input file size = 7510 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6162 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 = 6162 Output IDAT size = 6162 bytes (1270 bytes decrease) Output file size = 6240 bytes (1270 bytes = 16.91% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-48-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7445 bytes Input file size = 7523 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6182 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 = 6182 Output IDAT size = 6182 bytes (1263 bytes decrease) Output file size = 6260 bytes (1263 bytes = 16.79% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-49-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7940 bytes Input file size = 8018 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6533 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 = 6533 Output IDAT size = 6533 bytes (1407 bytes decrease) Output file size = 6611 bytes (1407 bytes = 17.55% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-50-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8705 bytes Input file size = 8795 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7098 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 = 7098 Output IDAT size = 7098 bytes (1607 bytes decrease) Output file size = 7176 bytes (1619 bytes = 18.41% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-51-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8332 bytes Input file size = 8422 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6889 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 = 6889 Output IDAT size = 6889 bytes (1443 bytes decrease) Output file size = 6967 bytes (1455 bytes = 17.28% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DrugUtilisation.Rcheck/vign_test/DrugUtilisation/vignettes/create_cohorts_files/figure-html/unnamed-chunk-52-1.png 672x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8356 bytes Input file size = 8446 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6922 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 = 6922 Output IDAT size = 6922 bytes (1434 bytes decrease) Output file size = 7000 bytes (1446 bytes = 17.12% decrease) --- finished re-building ‘create_cohorts.Rmd’ --- re-building ‘drug_utilisation.Rmd’ using rmarkdown Quitting from lines 277-278 [unnamed-chunk-9] (drug_utilisation.Rmd) Error: processing vignette 'drug_utilisation.Rmd' failed with diagnostics: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults' --- failed re-building ‘drug_utilisation.Rmd’ SUMMARY: processing the following file failed: ‘drug_utilisation.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-patched-linux-x86_64

Version: 0.7.1
Check: tests
Result: ERROR Running 'testthat.R' [120s] 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(DrugUtilisation) > > test_check("DrugUtilisation") Starting 2 test processes [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] ══ Skipped tests (50) ══════════════════════════════════════════════════════════ • On CRAN (50): 'test-benchmarkDrugUtilisation.R:2:3', 'test-addDrugUtilisation.R:3:3', 'test-addDrugUtilisation.R:156:3', 'test-addDrugUtilisation.R:196:3', 'test-dailyDose.R:2:3', 'test-generateDrugUtilisationCohortSet.R:2:3', 'test-generateDrugUtilisationCohortSet.R:23:3', 'test-generatedAtcCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:39:3', 'test-generatedIngredientCohortSet.R:54:3', 'test-generatedIngredientCohortSet.R:69:3', 'test-generatedIngredientCohortSet.R:98:3', 'test-drugUse.R:2:3', 'test-drugUse.R:42:3', 'test-drugUse.R:259:3', 'test-drugUse.R:463:3', 'test-drugUse.R:608:3', 'test-drugUse.R:860:3', 'test-drugUse.R:883:3', 'test-drugUse.R:932:3', 'test-drugUse.R:967:3', 'test-drugUse.R:1025:3', 'test-patterns.R:2:3', 'test-plotProportionOfPatientsCovered.R:2:3', 'test-plotProportionOfPatientsCovered.R:58:3', 'test-plotProportionOfPatientsCovered.R:100:3', 'test-plotTreatment.R:2:3', 'test-plots.R:2:3', 'test-readConceptList.R:2:3', 'test-require.R:2:3', 'test-require.R:143:3', 'test-require.R:324:3', 'test-require.R:432:3', 'test-require.R:526:3', 'test-require.R:597:3', 'test-indication.R:2:3', 'test-indication.R:202:3', 'test-indication.R:364:3', 'test-indication.R:481:3', 'test-summariseProportionOfPatientsCovered.R:94:3', 'test-summariseProportionOfPatientsCovered.R:170:3', 'test-summariseProportionOfPatientsCovered.R:277:3', 'test-summariseProportionOfPatientsCovered.R:497:3', 'test-summariseProportionOfPatientsCovered.R:550:3', 'test-tables.R:2:3', 'test-tables.R:132:3', 'test-tables.R:271:3', 'test-tables.R:393:3', 'test-tables.R:502:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-summariseDrugRestart.R:76:3'): summarise drug restart ──────── is.na(settings(resultsCohort)$censor_date) is not TRUE `actual`: `expected`: TRUE ── Failure ('test-summariseDrugRestart.R:83:3'): summarise drug restart ──────── unique(resultsSup$estimate_value) (`actual`) not equal to c(NA_character_, "0") (`expected`). `actual`: "-" "0" `expected`: NA "0" ── Failure ('test-summariseTreatment.R:49:3'): test summariseTreatment ───────── all(...) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-summariseDrugUtilisation.R:65:3'): summariseDrugUtilisation works ── all(...) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] Error: Test failures Execution halted Flavor: r-release-windows-x86_64

Version: 0.7.1
Check: tests
Result: ERROR Running 'testthat.R' [177s] 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(DrugUtilisation) > > test_check("DrugUtilisation") Starting 2 test processes [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] ══ Skipped tests (50) ══════════════════════════════════════════════════════════ • On CRAN (50): 'test-benchmarkDrugUtilisation.R:2:3', 'test-addDrugUtilisation.R:3:3', 'test-addDrugUtilisation.R:156:3', 'test-addDrugUtilisation.R:196:3', 'test-dailyDose.R:2:3', 'test-generateDrugUtilisationCohortSet.R:2:3', 'test-generateDrugUtilisationCohortSet.R:23:3', 'test-generatedAtcCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:2:3', 'test-generatedIngredientCohortSet.R:39:3', 'test-generatedIngredientCohortSet.R:54:3', 'test-generatedIngredientCohortSet.R:69:3', 'test-generatedIngredientCohortSet.R:98:3', 'test-drugUse.R:2:3', 'test-drugUse.R:42:3', 'test-drugUse.R:259:3', 'test-drugUse.R:463:3', 'test-drugUse.R:608:3', 'test-drugUse.R:860:3', 'test-drugUse.R:883:3', 'test-drugUse.R:932:3', 'test-drugUse.R:967:3', 'test-drugUse.R:1025:3', 'test-patterns.R:2:3', 'test-plotProportionOfPatientsCovered.R:2:3', 'test-plotProportionOfPatientsCovered.R:58:3', 'test-plotProportionOfPatientsCovered.R:100:3', 'test-plotTreatment.R:2:3', 'test-plots.R:2:3', 'test-readConceptList.R:2:3', 'test-require.R:2:3', 'test-require.R:143:3', 'test-require.R:324:3', 'test-require.R:432:3', 'test-require.R:526:3', 'test-require.R:597:3', 'test-indication.R:2:3', 'test-indication.R:202:3', 'test-indication.R:364:3', 'test-indication.R:481:3', 'test-summariseProportionOfPatientsCovered.R:94:3', 'test-summariseProportionOfPatientsCovered.R:170:3', 'test-summariseProportionOfPatientsCovered.R:277:3', 'test-summariseProportionOfPatientsCovered.R:497:3', 'test-summariseProportionOfPatientsCovered.R:550:3', 'test-tables.R:2:3', 'test-tables.R:132:3', 'test-tables.R:271:3', 'test-tables.R:393:3', 'test-tables.R:502:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-summariseDrugRestart.R:76:3'): summarise drug restart ──────── is.na(settings(resultsCohort)$censor_date) is not TRUE `actual`: `expected`: TRUE ── Failure ('test-summariseDrugRestart.R:83:3'): summarise drug restart ──────── unique(resultsSup$estimate_value) (`actual`) not equal to c(NA_character_, "0") (`expected`). `actual`: "-" "0" `expected`: NA "0" ── Failure ('test-summariseTreatment.R:49:3'): test summariseTreatment ───────── all(...) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-summariseDrugUtilisation.R:65:3'): summariseDrugUtilisation works ── all(...) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 4 | WARN 24 | SKIP 50 | PASS 69 ] Error: Test failures Execution halted Flavor: r-oldrel-windows-x86_64