Last updated on 2024-07-17 21:54:26 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.6.1 | 11.76 | 1342.83 | 1354.59 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.6.1 | 7.56 | 946.24 | 953.80 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.6.1 | 1121.05 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.6.1 | 873.71 | ERROR | |||
| r-devel-windows-x86_64 | 0.6.1 | 11.00 | 710.00 | 721.00 | ERROR | |
| r-patched-linux-x86_64 | 0.6.1 | 6.63 | 1343.47 | 1350.10 | OK | |
| r-release-linux-x86_64 | 0.6.1 | 6.30 | 1255.26 | 1261.56 | ERROR | |
| r-release-macos-arm64 | 0.6.1 | 287.00 | OK | |||
| r-release-macos-x86_64 | 0.6.1 | 762.00 | OK | |||
| r-release-windows-x86_64 | 0.6.1 | 10.00 | 704.00 | 714.00 | OK | |
| r-oldrel-macos-arm64 | 0.6.1 | 722.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 0.6.1 | 744.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.6.1 | 13.00 | 1023.00 | 1036.00 | ERROR |
Version: 0.6.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [544s/351s]
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 9 | SKIP 20 | PASS 146 ]
══ 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 ════════════════════════════════════════════════════════════════
── Error ('test-generatedAtcCohortSet.R:4:3'): test same results for ingredient cohorts ──
Error in `CodelistGenerator::getATCCodes(cdm, name = atcName, level = level,
doseForm = doseForm, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateAtcCohortSet(cdm = cdm, name = "test_cohort_1") at test-generatedAtcCohortSet.R:4:3
── Error ('test-generatedIngredientCohortSet.R:4:3'): test same results for ingredient cohorts ──
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:4:3
── Error ('test-generatedIngredientCohortSet.R:54:3'): date works ──────────────
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:54:3
── Error ('test-generatedIngredientCohortSet.R:77:3'): ingredient list and vector both work ──
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:77:3
[ FAIL 4 | WARN 9 | SKIP 20 | PASS 146 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.6.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [381s/351s]
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 9 | SKIP 20 | PASS 146 ]
══ 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-indication.R:3:3',
'test-indication.R:185:3', 'test-indication.R:339:3',
'test-indication.R:464:3', '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'
• empty test (1): 'test-generateConceptCohortSet.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-generatedAtcCohortSet.R:4:3'): test same results for ingredient cohorts ──
Error in `CodelistGenerator::getATCCodes(cdm, name = atcName, level = level,
doseForm = doseForm, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateAtcCohortSet(cdm = cdm, name = "test_cohort_1") at test-generatedAtcCohortSet.R:4:3
── Error ('test-generatedIngredientCohortSet.R:4:3'): test same results for ingredient cohorts ──
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:4:3
── Error ('test-generatedIngredientCohortSet.R:54:3'): date works ──────────────
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:54:3
── Error ('test-generatedIngredientCohortSet.R:77:3'): ingredient list and vector both work ──
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:77:3
[ FAIL 4 | WARN 9 | SKIP 20 | PASS 146 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.6.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [448s/232s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(DrugUtilisation)
>
> test_check("DrugUtilisation")
Starting 2 test processes
[ FAIL 4 | WARN 8 | SKIP 20 | PASS 146 ]
══ 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-indication.R:3:3',
'test-indication.R:185:3', 'test-indication.R:339:3',
'test-indication.R:464:3', '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'
• empty test (1): 'test-generateConceptCohortSet.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-generatedAtcCohortSet.R:4:3'): test same results for ingredient cohorts ──
Error in `CodelistGenerator::getATCCodes(cdm, name = atcName, level = level,
doseForm = doseForm, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateAtcCohortSet(cdm = cdm, name = "test_cohort_1") at test-generatedAtcCohortSet.R:4:3
── Error ('test-generatedIngredientCohortSet.R:4:3'): test same results for ingredient cohorts ──
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:4:3
── Error ('test-generatedIngredientCohortSet.R:54:3'): date works ──────────────
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:54:3
── Error ('test-generatedIngredientCohortSet.R:77:3'): ingredient list and vector both work ──
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:77:3
[ FAIL 4 | WARN 8 | SKIP 20 | PASS 146 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.6.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [376s/194s]
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 8 | SKIP 20 | PASS 146 ]
══ 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 ════════════════════════════════════════════════════════════════
── Error ('test-generatedAtcCohortSet.R:4:3'): test same results for ingredient cohorts ──
Error in `CodelistGenerator::getATCCodes(cdm, name = atcName, level = level,
doseForm = doseForm, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateAtcCohortSet(cdm = cdm, name = "test_cohort_1") at test-generatedAtcCohortSet.R:4:3
── Error ('test-generatedIngredientCohortSet.R:4:3'): test same results for ingredient cohorts ──
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:4:3
── Error ('test-generatedIngredientCohortSet.R:54:3'): date works ──────────────
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:54:3
── Error ('test-generatedIngredientCohortSet.R:77:3'): ingredient list and vector both work ──
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:77:3
[ FAIL 4 | WARN 8 | SKIP 20 | PASS 146 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.6.1
Check: tests
Result: ERROR
Running 'testthat.R' [181s]
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 9 | SKIP 20 | PASS 146 ]
══ 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 ════════════════════════════════════════════════════════════════
── Error ('test-generatedAtcCohortSet.R:4:3'): test same results for ingredient cohorts ──
Error in `CodelistGenerator::getATCCodes(cdm, name = atcName, level = level,
doseForm = doseForm, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateAtcCohortSet(cdm = cdm, name = "test_cohort_1") at test-generatedAtcCohortSet.R:4:3
── Error ('test-generatedIngredientCohortSet.R:4:3'): test same results for ingredient cohorts ──
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:4:3
── Error ('test-generatedIngredientCohortSet.R:54:3'): date works ──────────────
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:54:3
── Error ('test-generatedIngredientCohortSet.R:77:3'): ingredient list and vector both work ──
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:77:3
[ FAIL 4 | WARN 9 | SKIP 20 | PASS 146 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.6.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [506s/288s]
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 9 | SKIP 20 | PASS 146 ]
══ 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 ════════════════════════════════════════════════════════════════
── Error ('test-generatedAtcCohortSet.R:4:3'): test same results for ingredient cohorts ──
Error in `CodelistGenerator::getATCCodes(cdm, name = atcName, level = level,
doseForm = doseForm, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateAtcCohortSet(cdm = cdm, name = "test_cohort_1") at test-generatedAtcCohortSet.R:4:3
── Error ('test-generatedIngredientCohortSet.R:4:3'): test same results for ingredient cohorts ──
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:4:3
── Error ('test-generatedIngredientCohortSet.R:54:3'): date works ──────────────
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:54:3
── Error ('test-generatedIngredientCohortSet.R:77:3'): ingredient list and vector both work ──
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:77:3
[ FAIL 4 | WARN 9 | SKIP 20 | PASS 146 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.6.1
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘a01_introCreateCohort.Rmd’
...
"duckdb_connection#ANY" would also be valid
> conceptSet_json <- codesFromConceptSet(here::here("inst/Concept"),
+ cdm)
When sourcing ‘a01_introCreateCohort.R’:
Error: Invalid path:
/private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/RtmpHM92Kg/file96fb32167096/vignettes/inst/Concept
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
‘a01_introCreateCohort.Rmd’ using ‘UTF-8’... failed
‘a02_scalingOfInstantiateCohorts.Rmd’ using ‘UTF-8’... [0s/1s] OK
‘a03_addIndications-example.Rmd’ using ‘UTF-8’... [24s/38s] OK
‘a04_addDrugInfo.Rmd’ using ‘UTF-8’... [64s/135s] OK
‘a05_treatmentDiscontinuation.Rmd’ using ‘UTF-8’... [0s/1s] OK
‘a06_treatmentSummary.Rmd’ using ‘UTF-8’... [10s/31s] OK
‘a07_characteriseACohort.Rmd’ using ‘UTF-8’... [0s/1s] OK
‘routePatternDose.Rmd’ using ‘UTF-8’... [28s/79s] OK
Flavor: r-oldrel-macos-arm64
Version: 0.6.1
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘a01_introCreateCohort.Rmd’
...
"duckdb_connection#ANY" would also be valid
> conceptSet_json <- codesFromConceptSet(here::here("inst/Concept"),
+ cdm)
When sourcing ‘a01_introCreateCohort.R’:
Error: Invalid path:
/private/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T/RtmpLr5SOh/file52ea7e3e58d2/vignettes/inst/Concept
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
‘a01_introCreateCohort.Rmd’ using ‘UTF-8’... failed
‘a02_scalingOfInstantiateCohorts.Rmd’ using ‘UTF-8’... [0s/0s] OK
‘a03_addIndications-example.Rmd’ using ‘UTF-8’... [33s/39s] OK
‘a04_addDrugInfo.Rmd’ using ‘UTF-8’... [84s/94s] OK
‘a05_treatmentDiscontinuation.Rmd’ using ‘UTF-8’... [0s/0s] OK
‘a06_treatmentSummary.Rmd’ using ‘UTF-8’... [13s/15s] OK
‘a07_characteriseACohort.Rmd’ using ‘UTF-8’... [0s/0s] OK
‘routePatternDose.Rmd’ using ‘UTF-8’... [33s/33s] OK
Flavor: r-oldrel-macos-x86_64
Version: 0.6.1
Check: tests
Result: ERROR
Running 'testthat.R' [268s]
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 9 | SKIP 20 | PASS 146 ]
══ 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 ════════════════════════════════════════════════════════════════
── Error ('test-generatedAtcCohortSet.R:4:3'): test same results for ingredient cohorts ──
Error in `CodelistGenerator::getATCCodes(cdm, name = atcName, level = level,
doseForm = doseForm, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateAtcCohortSet(cdm = cdm, name = "test_cohort_1") at test-generatedAtcCohortSet.R:4:3
── Error ('test-generatedIngredientCohortSet.R:4:3'): test same results for ingredient cohorts ──
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:4:3
── Error ('test-generatedIngredientCohortSet.R:54:3'): date works ──────────────
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:54:3
── Error ('test-generatedIngredientCohortSet.R:77:3'): ingredient list and vector both work ──
Error in `CodelistGenerator::getDrugIngredientCodes(cdm = cdm, name = ingredient,
doseForm = doseForm, ingredientRange = ingredientRange, withConceptDetails = FALSE)`: unused argument (withConceptDetails = FALSE)
Backtrace:
▆
1. └─DrugUtilisation::generateIngredientCohortSet(...) at test-generatedIngredientCohortSet.R:77:3
[ FAIL 4 | WARN 9 | SKIP 20 | PASS 146 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64