Last updated on 2024-12-18 19:49:42 CET.
| Package | FAIL | ERROR | NOTE | OK |
|---|---|---|---|---|
| CohortCharacteristics | 6 | 7 | ||
| DrugUtilisation | 1 | 12 | ||
| omopgenerics | 1 | 12 | ||
| OmopViewer | 13 | |||
| PatientProfiles | 13 |
Current CRAN status: NOTE: 6, OK: 7
Version: 0.4.0
Check: installed package size
Result: NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 3.5Mb
help 1.9Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: ERROR: 1, OK: 12
Version: 0.7.1
Check: dependencies in R code
Result: WARN
Missing or unexported object: 'visOmopResults::optionsVisOmopTable'
Flavor: r-release-windows-x86_64
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
Flavor: r-release-windows-x86_64
Version: 0.7.1
Check: tests
Result: ERROR
Running 'testthat.R' [121s]
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: 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
Flavor: r-release-windows-x86_64
Current CRAN status: FAIL: 1, OK: 12
Version: 0.4.1
Check: PDF version of manual
Result: FAIL
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
+ )
>
> x |>
+ uniteStrata(c("sex", "age_group"))
# A tibble: 4 × 4
variable value strata_name strata_level
<chr> <dbl> <chr> <chr>
1 number subjects 10 sex &&& age_group Male &&& <40
2 number subjects 15 sex &&& age_group Female &&& >40
3 number subjects 40 sex &&& age_group Male &&& >40
4 number subjects 78 sex &&& age_group Female &&& <40
>
>
>
>
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed: 17.8 0.94 18.75 NA NA
> grDevices::dev.off()
null device
1
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Flavor: r-devel-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13