Last updated on 2024-05-01 03:54:15 CEST.
| Package | ERROR | OK |
|---|---|---|
| CohortCharacteristics | 2 | 11 |
| DrugUtilisation | 2 | 11 |
| omopgenerics | 13 | |
| PatientProfiles | 13 |
Current CRAN status: ERROR: 2, OK: 11
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [116s/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(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 5 | WARN 0 | SKIP 13 | PASS 5 ]
══ Skipped tests (13) ══════════════════════════════════════════════════════════
• On CRAN (12): 'test-plotCharacteristics.R:2:3',
'test-plotLargeScaleCharacteristics.R:3:3', 'test-plotSummarised.R:2:3',
'test-plotSummarised.R:82:3', 'test-plotSummarised.R:179:3',
'test-plotSummarised.R:263:3', 'test-summariseCohortIntersect.R:2:3',
'test-summariseCohortOverlap.R:2:3', 'test-summariseCohortTiming.R:2:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableSummarised.R:2:3', 'test-tableSummarised.R:114:3'
• empty test (1): 'test-tableSummarised.R:235:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-summariseCharacteristics.R:76:3'): test summariseCharacteristics ──
Expected `... <- NULL` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
── Error ('test-summariseCharacteristics.R:88:3'): test summariseCharacteristics ──
Error in `eval(code, test_env)`: object 'result' not found
Backtrace:
▆
1. ├─testthat::expect_true(inherits(result, "summarised_result")) at test-summariseCharacteristics.R:88:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::inherits(result, "summarised_result")
── Failure ('test-summariseCharacteristics.R:291:3'): test empty cohort ────────
Expected `summariseCharacteristics(...)` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
── Failure ('test-summariseCharacteristics.R:301:3'): test empty cohort ────────
Expected `... <- NULL` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
── Failure ('test-summariseCharacteristics.R:308:3'): test empty cohort ────────
Expected `... <- NULL` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
[ FAIL 5 | WARN 0 | SKIP 13 | PASS 5 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘a06_summarisePatientCharacteristics.Rmd’ using rmarkdown
Quitting from lines at lines 27-109 [unnamed-chunk-2] (a06_summarisePatientCharacteristics.Rmd)
Error: processing vignette 'a06_summarisePatientCharacteristics.Rmd' failed with diagnostics:
Can't select columns that don't exist.
✖ Column `result_type` doesn't exist.
--- failed re-building ‘a06_summarisePatientCharacteristics.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a08_summariseCohortOverlap.Rmd’ using rmarkdown
--- finished re-building ‘a08_summariseCohortOverlap.Rmd’
SUMMARY: processing the following file failed:
‘a06_summarisePatientCharacteristics.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [109s/113s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 5 | WARN 0 | SKIP 13 | PASS 5 ]
══ Skipped tests (13) ══════════════════════════════════════════════════════════
• On CRAN (12): 'test-plotCharacteristics.R:2:3',
'test-plotLargeScaleCharacteristics.R:3:3', 'test-plotSummarised.R:2:3',
'test-plotSummarised.R:82:3', 'test-plotSummarised.R:179:3',
'test-plotSummarised.R:263:3', 'test-summariseCohortIntersect.R:2:3',
'test-summariseCohortOverlap.R:2:3', 'test-summariseCohortTiming.R:2:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableSummarised.R:2:3', 'test-tableSummarised.R:114:3'
• empty test (1): 'test-tableSummarised.R:235:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-summariseCharacteristics.R:76:3'): test summariseCharacteristics ──
Expected `... <- NULL` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
── Error ('test-summariseCharacteristics.R:88:3'): test summariseCharacteristics ──
Error in `eval(code, test_env)`: object 'result' not found
Backtrace:
▆
1. ├─testthat::expect_true(inherits(result, "summarised_result")) at test-summariseCharacteristics.R:88:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::inherits(result, "summarised_result")
── Failure ('test-summariseCharacteristics.R:291:3'): test empty cohort ────────
Expected `summariseCharacteristics(...)` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
── Failure ('test-summariseCharacteristics.R:301:3'): test empty cohort ────────
Expected `... <- NULL` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
── Failure ('test-summariseCharacteristics.R:308:3'): test empty cohort ────────
Expected `... <- NULL` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
[ FAIL 5 | WARN 0 | SKIP 13 | PASS 5 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Current CRAN status: ERROR: 2, OK: 11
Version: 0.5.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [523s/296s]
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 3 | WARN 71 | SKIP 20 | PASS 154 ]
══ Skipped tests (20) ══════════════════════════════════════════════════════════
• On CRAN (19): 'test-benchmarkDUS.R:2:3', 'test-dailyDose.R:2:3',
'test-generateDrugUtilisationCohortSet.R:48:3',
'test-generateDrugUtilisationCohortSet.R:147:3',
'test-generateDrugUtilisationCohortSet.R:203:3',
'test-generateDrugUtilisationCohortSet.R:253:3',
'test-generateDrugUtilisationCohortSet.R:349:3', 'test-drugUse.R:2:3',
'test-drugUse.R:40:3', 'test-drugUse.R:254:3', 'test-drugUse.R:455:3',
'test-drugUse.R:597:3', 'test-drugUse.R:847:3', 'test-drugUse.R:868:3',
'test-drugUse.R:914:3', 'test-indication.R:3:3', 'test-indication.R:185:3',
'test-indication.R:339:3', 'test-indication.R:464:3'
• empty test (1): 'test-generateConceptCohortSet.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-indication.R:648:3'): summariseIndication ────────────────────
grepl("summarised_indication", unique(result$result_type)) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test-largeScaleCharacteristics.R:8:3'): basic functionality summariseCodelist ──
Expected `summariseCharacteristicsFromCodelist(cdm[["cohort1"]], conceptSet = conceptSet)` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
── Failure ('test-largeScaleCharacteristics.R:14:3'): basic functionality summariseCodelist ──
Expected `summariseCharacteristicsFromCodelist(...)` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
[ FAIL 3 | WARN 71 | SKIP 20 | PASS 154 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.5.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [503s/267s]
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 3 | WARN 71 | SKIP 20 | PASS 154 ]
══ Skipped tests (20) ══════════════════════════════════════════════════════════
• On CRAN (19): 'test-benchmarkDUS.R:2:3', 'test-dailyDose.R:2:3',
'test-generateDrugUtilisationCohortSet.R:48:3',
'test-generateDrugUtilisationCohortSet.R:147:3',
'test-generateDrugUtilisationCohortSet.R:203:3',
'test-generateDrugUtilisationCohortSet.R:253:3',
'test-generateDrugUtilisationCohortSet.R:349:3', 'test-drugUse.R:2:3',
'test-drugUse.R:40:3', 'test-drugUse.R:254:3', 'test-drugUse.R:455:3',
'test-drugUse.R:597:3', 'test-drugUse.R:847:3', 'test-drugUse.R:868:3',
'test-drugUse.R:914:3', 'test-indication.R:3:3', 'test-indication.R:185:3',
'test-indication.R:339:3', 'test-indication.R:464:3'
• empty test (1): 'test-generateConceptCohortSet.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-indication.R:648:3'): summariseIndication ────────────────────
grepl("summarised_indication", unique(result$result_type)) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test-largeScaleCharacteristics.R:8:3'): basic functionality summariseCodelist ──
Expected `summariseCharacteristicsFromCodelist(cdm[["cohort1"]], conceptSet = conceptSet)` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
── Failure ('test-largeScaleCharacteristics.R:14:3'): basic functionality summariseCodelist ──
Expected `summariseCharacteristicsFromCodelist(...)` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
[ FAIL 3 | WARN 71 | SKIP 20 | PASS 154 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Current CRAN status: OK: 13
Current CRAN status: OK: 13