Last updated on 2024-11-29 00:49:32 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.7.1 | 8.38 | 495.22 | 503.60 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.7.1 | 5.83 | 365.56 | 371.39 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.7.1 | 835.19 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.7.1 | 883.55 | ERROR | |||
| r-devel-windows-x86_64 | 0.7.1 | 11.00 | 307.00 | 318.00 | ERROR | |
| r-patched-linux-x86_64 | 0.7.1 | 10.79 | 469.68 | 480.47 | 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 | 348.00 | 359.00 | 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 | 14.00 | 447.00 | 461.00 | ERROR |
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-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’ [281s/163s]
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’ [216s/159s]
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-dailyDose.R:2:3', 'test-benchmarkDrugUtilisation.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-oldrel-windows-x86_64
Version: 0.7.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [444s/275s]
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’ [462s/270s]
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' [116s]
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-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-oldrel-windows-x86_64
Version: 0.7.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [263s/149s]
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' [122s]
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' [179s]
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