Last updated on 2024-07-27 11:49:25 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| CohortCharacteristics | 8 | 5 | |
| DrugUtilisation | 11 | 2 | |
| omopgenerics | 2 | 11 | |
| PatientProfiles | 9 | 4 |
Current CRAN status: NOTE: 8, OK: 5
Version: 0.2.1
Check: installed package size
Result: NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
doc 5.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, 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: 11, OK: 2
Version: 0.6.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [555s/358s]
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-debian-clang
Version: 0.6.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [386s/210s]
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-debian-gcc
Version: 0.6.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [642s/344s]
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-clang
Version: 0.6.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [600s/324s]
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-gcc
Version: 0.6.1
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 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-windows-x86_64
Version: 0.6.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [523s/323s]
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-patched-linux-x86_64
Version: 0.6.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [508s/301s]
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-release-linux-x86_64
Version: 0.6.1
Check: tests
Result: ERROR
Running 'testthat.R' [173s]
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-release-windows-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/RtmpQSsmHW/file15b26514b789f/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’... [23s/28s] OK
‘a04_addDrugInfo.Rmd’ using ‘UTF-8’... [57s/65s] OK
‘a05_treatmentDiscontinuation.Rmd’ using ‘UTF-8’... [0s/0s] OK
‘a06_treatmentSummary.Rmd’ using ‘UTF-8’... [9s/10s] OK
‘a07_characteriseACohort.Rmd’ using ‘UTF-8’... [0s/0s] OK
‘routePatternDose.Rmd’ using ‘UTF-8’... [25s/31s] 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/RtmpJnYIk9/file831a29e763e6/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’... [36s/59s] OK
‘a04_addDrugInfo.Rmd’ using ‘UTF-8’... [90s/126s] OK
‘a05_treatmentDiscontinuation.Rmd’ using ‘UTF-8’... [0s/0s] OK
‘a06_treatmentSummary.Rmd’ using ‘UTF-8’... [14s/20s] OK
‘a07_characteriseACohort.Rmd’ using ‘UTF-8’... [0s/0s] OK
‘routePatternDose.Rmd’ using ‘UTF-8’... [37s/44s] OK
Flavor: r-oldrel-macos-x86_64
Version: 0.6.1
Check: tests
Result: ERROR
Running 'testthat.R' [265s]
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-oldrel-windows-x86_64
Current CRAN status: ERROR: 2, OK: 11
Version: 0.2.3
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘a02_concept_set.Rmd’
...
> condition_codes <- list(c(201820, 4087682, 3655269))
> newCodelist(condition_codes)
When sourcing ‘a02_concept_set.R’:
Error: ! `x` must be named.
`x` must be a list with objects of class numeric, integer, and integer64; it
can not contain NA; it has to be named; it can not be NULL.
Execution halted
‘a01_cdm_reference.Rmd’ using ‘UTF-8’... [1s/1s] OK
‘a02_concept_set.Rmd’ using ‘UTF-8’... failed
‘a03_cohort_table.Rmd’ using ‘UTF-8’... [4s/4s] OK
‘a04_summarised_result.Rmd’ using ‘UTF-8’... [1s/1s] OK
‘reexport.Rmd’ using ‘UTF-8’... [0s/0s] OK
Flavor: r-oldrel-macos-arm64
Version: 0.2.3
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘a02_concept_set.Rmd’
...
> condition_codes <- list(c(201820, 4087682, 3655269))
> newCodelist(condition_codes)
When sourcing ‘a02_concept_set.R’:
Error: ! `x` must be named.
`x` must be a list with objects of class numeric, integer, and integer64; it
can not contain NA; it has to be named; it can not be NULL.
Execution halted
‘a01_cdm_reference.Rmd’ using ‘UTF-8’... [1s/1s] OK
‘a02_concept_set.Rmd’ using ‘UTF-8’... failed
‘a03_cohort_table.Rmd’ using ‘UTF-8’... [6s/10s] OK
‘a04_summarised_result.Rmd’ using ‘UTF-8’... [2s/4s] OK
‘reexport.Rmd’ using ‘UTF-8’... [0s/0s] OK
Flavor: r-oldrel-macos-x86_64
Current CRAN status: ERROR: 9, OK: 4
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘cohort-intersect.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/PatientProfiles.Rcheck/vign_test/PatientProfiles/vignettes/cohort-intersect_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 16730 bytes
Input file size = 16832 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0
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 IDAT size = 14956
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 = 5 IDAT size = 14956
Output IDAT size = 14956 bytes (1774 bytes decrease)
Output file size = 15034 bytes (1798 bytes = 10.68% decrease)
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- finished re-building ‘cohort-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘concept-intersect.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 161-195 [unnamed-chunk-11] (concept-intersect.Rmd)
Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics:
ℹ In argument: `acetaminophen_minf_to_inf`
Caused by error:
! Object `acetaminophen_minf_to_inf` not found.
--- failed re-building ‘concept-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘demographics.rmd’ using rmarkdown
--- finished re-building ‘demographics.rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘summarise.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘summarise.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘table-intersect.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘table-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
‘concept-intersect.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘cohort-intersect.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PatientProfiles.Rcheck/vign_test/PatientProfiles/vignettes/cohort-intersect_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 16730 bytes
Input file size = 16832 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0
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 IDAT size = 14956
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 = 5 IDAT size = 14956
Output IDAT size = 14956 bytes (1774 bytes decrease)
Output file size = 15034 bytes (1798 bytes = 10.68% decrease)
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- finished re-building ‘cohort-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘concept-intersect.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 161-195 [unnamed-chunk-11] (concept-intersect.Rmd)
Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics:
ℹ In argument: `acetaminophen_minf_to_inf`
Caused by error:
! Object `acetaminophen_minf_to_inf` not found.
--- failed re-building ‘concept-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘demographics.rmd’ using rmarkdown
--- finished re-building ‘demographics.rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘summarise.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘summarise.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘table-intersect.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘table-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
‘concept-intersect.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘cohort-intersect.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/PatientProfiles.Rcheck/vign_test/PatientProfiles/vignettes/cohort-intersect_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 16730 bytes
Input file size = 16832 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0
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 IDAT size = 14956
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 = 5 IDAT size = 14956
Output IDAT size = 14956 bytes (1774 bytes decrease)
Output file size = 15034 bytes (1798 bytes = 10.68% decrease)
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- finished re-building ‘cohort-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘concept-intersect.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 161-195 [unnamed-chunk-11] (concept-intersect.Rmd)
Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics:
ℹ In argument: `acetaminophen_minf_to_inf`
Caused by error:
! Object `acetaminophen_minf_to_inf` not found.
--- failed re-building ‘concept-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘demographics.rmd’ using rmarkdown
--- finished re-building ‘demographics.rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘summarise.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘summarise.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘table-intersect.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘table-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
‘concept-intersect.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘cohort-intersect.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/PatientProfiles.Rcheck/vign_test/PatientProfiles/vignettes/cohort-intersect_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 16730 bytes
Input file size = 16832 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0
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 IDAT size = 14956
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 = 5 IDAT size = 14956
Output IDAT size = 14956 bytes (1774 bytes decrease)
Output file size = 15034 bytes (1798 bytes = 10.68% decrease)
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- finished re-building ‘cohort-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘concept-intersect.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 161-195 [unnamed-chunk-11] (concept-intersect.Rmd)
Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics:
ℹ In argument: `acetaminophen_minf_to_inf`
Caused by error:
! Object `acetaminophen_minf_to_inf` not found.
--- failed re-building ‘concept-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘demographics.rmd’ using rmarkdown
--- finished re-building ‘demographics.rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘summarise.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘summarise.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘table-intersect.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘table-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
‘concept-intersect.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'cohort-intersect.Rmd' using rmarkdown
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- finished re-building 'cohort-intersect.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'concept-intersect.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 161-195 [unnamed-chunk-11] (concept-intersect.Rmd)
Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics:
ℹ In argument: `acetaminophen_minf_to_inf`
Caused by error:
! Object `acetaminophen_minf_to_inf` not found.
--- failed re-building 'concept-intersect.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'demographics.rmd' using rmarkdown
--- finished re-building 'demographics.rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'summarise.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building 'summarise.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'table-intersect.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building 'table-intersect.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
'concept-intersect.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘cohort-intersect.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PatientProfiles.Rcheck/vign_test/PatientProfiles/vignettes/cohort-intersect_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 16730 bytes
Input file size = 16832 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0
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 IDAT size = 14956
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 = 5 IDAT size = 14956
Output IDAT size = 14956 bytes (1774 bytes decrease)
Output file size = 15034 bytes (1798 bytes = 10.68% decrease)
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- finished re-building ‘cohort-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘concept-intersect.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 161-195 [unnamed-chunk-11] (concept-intersect.Rmd)
Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics:
ℹ In argument: `acetaminophen_minf_to_inf`
Caused by error:
! Object `acetaminophen_minf_to_inf` not found.
--- failed re-building ‘concept-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘demographics.rmd’ using rmarkdown
--- finished re-building ‘demographics.rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘summarise.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘summarise.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘table-intersect.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘table-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
‘concept-intersect.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘cohort-intersect.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/PatientProfiles.Rcheck/vign_test/PatientProfiles/vignettes/cohort-intersect_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 16730 bytes
Input file size = 16832 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0
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 IDAT size = 14956
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 = 5 IDAT size = 14956
Output IDAT size = 14956 bytes (1774 bytes decrease)
Output file size = 15034 bytes (1798 bytes = 10.68% decrease)
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- finished re-building ‘cohort-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘concept-intersect.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 161-195 [unnamed-chunk-11] (concept-intersect.Rmd)
Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics:
ℹ In argument: `acetaminophen_minf_to_inf`
Caused by error:
! Object `acetaminophen_minf_to_inf` not found.
--- failed re-building ‘concept-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘demographics.rmd’ using rmarkdown
--- finished re-building ‘demographics.rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘summarise.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘summarise.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘table-intersect.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘table-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
‘concept-intersect.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64