Last updated on 2025-12-07 18:49:39 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.5.0 | 7.31 | 585.81 | 593.12 | OK | |
| r-devel-linux-x86_64-debian-gcc | 3.5.0 | 5.12 | 274.93 | 280.05 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 3.5.0 | 15.00 | 900.17 | 915.17 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 3.5.0 | 13.00 | 881.33 | 894.33 | OK | |
| r-devel-windows-x86_64 | 3.5.0 | 9.00 | 388.00 | 397.00 | OK | |
| r-patched-linux-x86_64 | 3.5.0 | 6.57 | 561.01 | 567.58 | OK | |
| r-release-linux-x86_64 | 3.5.0 | 7.40 | 561.36 | 568.76 | OK | |
| r-release-macos-arm64 | 3.5.0 | OK | ||||
| r-release-macos-x86_64 | 3.5.0 | 11.00 | 280.00 | 291.00 | OK | |
| r-release-windows-x86_64 | 3.5.0 | 9.00 | 399.00 | 408.00 | OK | |
| r-oldrel-macos-arm64 | 3.5.0 | OK | ||||
| r-oldrel-macos-x86_64 | 3.5.0 | 8.00 | 262.00 | 270.00 | OK | |
| r-oldrel-windows-x86_64 | 3.5.0 | 14.00 | 565.00 | 579.00 | OK |
Version: 3.5.0
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'covr', 'visOmopResults', 'knitr', 'rmarkdown', 'spelling', 'gt',
'flextable'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 3.5.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [236s/118s]
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(CodelistGenerator)
>
> test_check("CodelistGenerator")
Starting 2 test processes.
> test-codesInUse.R: Limiting to domains of interest
> test-codesInUse.R: Getting concepts to include
> test-codesInUse.R: Search completed. Finishing up.
> test-codesInUse.R: v 3 candidate concepts identified
> test-codesInUse.R: Time taken: 0 minutes and 0 seconds
> test-codesInUse.R: No codes from codelist cs2 found in the database
> test-codesInUse.R: Limiting to domains of interest
> test-codesInUse.R: Getting concepts to include
> test-codesInUse.R: Search completed. Finishing up.
> test-codesInUse.R: v 1 candidate concept identified
> test-codesInUse.R: Time taken: 0 minutes and 0 seconds
> test-compareCodelists.R: Limiting to domains of interest
> test-compareCodelists.R: Getting concepts to include
> test-compareCodelists.R: Adding descendants
> test-compareCodelists.R: Search completed. Finishing up.
> test-compareCodelists.R: v 3 candidate concepts identified
> test-compareCodelists.R: Time taken: 0 minutes and 0 seconds
> test-compareCodelists.R: Limiting to domains of interest
> test-compareCodelists.R: Getting concepts to include
> test-compareCodelists.R: Adding descendants
> test-compareCodelists.R: Search completed. Finishing up.
> test-compareCodelists.R: v 2 candidate concepts identified
> test-compareCodelists.R: Time taken: 0 minutes and 1 seconds
> test-compareCodelists.R: Limiting to domains of interest
> test-compareCodelists.R: Getting concepts to include
> test-compareCodelists.R: Adding descendants
> test-compareCodelists.R: Search completed. Finishing up.
> test-compareCodelists.R: v 3 candidate concepts identified
> test-compareCodelists.R: Time taken: 0 minutes and 0 seconds
> test-compareCodelists.R: Limiting to domains of interest
> test-compareCodelists.R: Getting concepts to include
> test-compareCodelists.R: Adding concepts using synonymns
> test-compareCodelists.R: Adding descendants
> test-compareCodelists.R: Search completed. Finishing up.
> test-compareCodelists.R: v 4 candidate concepts identified
> test-compareCodelists.R: Time taken: 0 minutes and 2 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 1 candidate concept identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 2 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 5 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Adding ancestor
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 4 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 1 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Adding ancestor
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 2 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 1 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 5 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 1 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding concepts using synonymns
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 4 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 2 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 2 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 1 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 2 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 2 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 2 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 2 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding codes from non-standard
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 2 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 2 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding codes from non-standard
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 1 candidate concept identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 1 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding concepts using synonymns
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Adding ancestor
> test-getCandidateCodes.R: Adding codes from non-standard
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 5 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 3 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding concepts using synonymns
> test-getCandidateCodes.R: Adding ancestor
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 1 candidate concept identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 2 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding concepts using synonymns
> test-getCandidateCodes.R: Adding descendants
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getCandidateCodes.R: Adding ancestor
> test-getICD10StandardCodes.R: Mapping from non-standard to standard concepts
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 9 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 3 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getICD10StandardCodes.R: Getting descendant concepts
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getCandidateCodes.R: Getting concepts to include
> test-getICD10StandardCodes.R: Mapping from non-standard to standard concepts
> test-getCandidateCodes.R: Adding concepts using synonymns
> test-getICD10StandardCodes.R: Getting descendant concepts
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getICD10StandardCodes.R: Mapping from non-standard to standard concepts
> test-getICD10StandardCodes.R: Getting descendant concepts
> test-getCandidateCodes.R: Adding descendants
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getICD10StandardCodes.R: Mapping from non-standard to standard concepts
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getICD10StandardCodes.R: Mapping from non-standard to standard concepts
> test-getCandidateCodes.R: Adding ancestor
> test-getICD10StandardCodes.R: Getting descendant concepts
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getICD10StandardCodes.R: Mapping from non-standard to standard concepts
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 10 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 3 seconds
> test-getICD10StandardCodes.R: Getting descendant concepts
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getCandidateCodes.R: Getting concepts to include
> test-getICD10StandardCodes.R:
> test-getICD10StandardCodes.R: -- No codes found --
> test-getICD10StandardCodes.R:
> test-getICD10StandardCodes.R: i No ICD-10 chapter codes were found in the concept table.
> test-getICD10StandardCodes.R: -- Were ICD-10 codes included when loading vocabularies into the database?
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getICD10StandardCodes.R: Mapping from non-standard to standard concepts
> test-getCandidateCodes.R: No codes found for the given search strategy
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getICD10StandardCodes.R: Getting descendant concepts
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 1 candidate concept identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getICD10StandardCodes.R: Mapping from non-standard to standard concepts
> test-getICD10StandardCodes.R: Getting descendant concepts
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getCandidateCodes.R: No codes found for the given search strategy
> test-getICD10StandardCodes.R: Mapping from non-standard to standard concepts
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getICD10StandardCodes.R: Getting descendant concepts
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getICD10StandardCodes.R: Mapping from non-standard to standard concepts
> test-getICD10StandardCodes.R: Getting descendant concepts
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getICD10StandardCodes.R: Mapping from non-standard to standard concepts
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getCandidateCodes.R: Getting concepts to include
> test-getICD10StandardCodes.R: Mapping from non-standard to standard concepts
> test-getICD10StandardCodes.R: Getting descendant concepts
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getICD10StandardCodes.R: Mapping from non-standard to standard concepts
> test-getICD10StandardCodes.R: Getting descendant concepts
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getICD10StandardCodes.R:
> test-getICD10StandardCodes.R: -- No codes found --
> test-getICD10StandardCodes.R:
> test-getICD10StandardCodes.R: i No ICD-10 chapter codes were found in the concept table.
> test-getICD10StandardCodes.R: -- Were ICD-10 codes included when loading vocabularies into the database?
> test-getICD10StandardCodes.R: Getting non-standard ICD10 concepts
> test-getICD10StandardCodes.R: Mapping from non-standard to standard concepts
> test-getICD10StandardCodes.R: Getting descendant concepts
> test-getCandidateCodes.R: No codes found for the given search strategy
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 1 candidate concept identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 2 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 5 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Adding ancestor
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 4 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Adding ancestor
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 2 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 5 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding concepts using synonymns
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 4 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 2 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 2 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 2 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding codes from non-standard
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 2 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding codes from non-standard
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 1 candidate concept identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding concepts using synonymns
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Adding ancestor
> test-getCandidateCodes.R: Adding codes from non-standard
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 5 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getICD10StandardCodes.R:
> test-getICD10StandardCodes.R: -- No codes found --
> test-getCandidateCodes.R: Getting concepts to include
> test-getICD10StandardCodes.R:
> test-getICD10StandardCodes.R: i No ICD-10 chapter codes were found in the concept table.
> test-getICD10StandardCodes.R: -- Were ICD-10 codes included when loading vocabularies into the database?
> test-getCandidateCodes.R: Adding concepts using synonymns
> test-getCandidateCodes.R: Adding ancestor
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 1 candidate concept identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding concepts using synonymns
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Adding ancestor
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 9 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Adding concepts using synonymns
> test-getCandidateCodes.R: Adding descendants
> test-getCandidateCodes.R: Adding ancestor
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 10 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: No codes found for the given search strategy
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 1 candidate concept identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: No codes found for the given search strategy
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: No codes found for the given search strategy
> test-getICD10StandardCodes.R:
> test-getICD10StandardCodes.R: -- No codes found --
> test-getICD10StandardCodes.R:
> test-getICD10StandardCodes.R: i No ICD-10 chapter codes were found in the concept table.
> test-getICD10StandardCodes.R: -- Were ICD-10 codes included when loading vocabularies into the database?
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 4 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getMappings.R: Limiting to domains of interest
> test-getCandidateCodes.R: v 3 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getMappings.R: Getting concepts to include
> test-getMappings.R: Adding descendants
> test-getMappings.R: Search completed. Finishing up.
> test-getMappings.R: v 5 candidate concepts identified
> test-getMappings.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 4 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-getCandidateCodes.R: Limiting to domains of interest
> test-getCandidateCodes.R: Getting concepts to include
> test-getCandidateCodes.R: Search completed. Finishing up.
> test-getCandidateCodes.R: v 3 candidate concepts identified
> test-getCandidateCodes.R: Time taken: 0 minutes and 0 seconds
> test-restrictToCodesInUse.R: No codes from codelist b found in the database
> test-restrictToCodesInUse.R: No codes from codelist b found in the database
> test-restrictToCodesInUse.R: No codes from codelist a found in the database
> test-restrictToCodesInUse.R: No codes from codelist b found in the database
> test-stratifyByDoseUnit.R: Limiting to domains of interest
> test-stratifyByDoseUnit.R: Getting concepts to include
> test-stratifyByDoseUnit.R: Adding descendants
> test-stratifyByDoseUnit.R: Search completed. Finishing up.
> test-stratifyByDoseUnit.R: v 2 candidate concepts identified
> test-stratifyByDoseUnit.R: Time taken: 0 minutes and 0 seconds
> test-stratifyByRouteCategory.R: Limiting to domains of interest
> test-stratifyByRouteCategory.R: Getting concepts to include
> test-stratifyByRouteCategory.R: Adding descendants
> test-stratifyByRouteCategory.R: Search completed. Finishing up.
> test-stratifyByRouteCategory.R: v 2 candidate concepts identified
> test-stratifyByRouteCategory.R: Time taken: 0 minutes and 0 seconds
> test-stratifyByRouteCategory.R: Limiting to domains of interest
> test-stratifyByRouteCategory.R: Getting concepts to include
> test-stratifyByRouteCategory.R: Adding descendants
> test-stratifyByRouteCategory.R: Search completed. Finishing up.
> test-stratifyByRouteCategory.R: v 2 candidate concepts identified
> test-stratifyByRouteCategory.R: Time taken: 0 minutes and 0 seconds
> test-summariseAchillesCodeUse.R: Limiting to domains of interest
> test-summariseAchillesCodeUse.R: Getting concepts to include
> test-summariseAchillesCodeUse.R: Adding descendants
> test-summariseAchillesCodeUse.R: Search completed. Finishing up.
> test-summariseAchillesCodeUse.R: v 2 candidate concepts identified
> test-summariseAchillesCodeUse.R: Time taken: 0 minutes and 0 seconds
> test-summariseAchillesCodeUse.R:
> test-summariseAchillesCodeUse.R:
> test-summariseAchillesCodeUse.R: i No achilles counts found for the concepts provided.
> test-summariseAchillesCodeUse.R:
> test-summariseOrphanCodes.R: Limiting to domains of interest
> test-summariseOrphanCodes.R: Getting concepts to include
> test-summariseOrphanCodes.R: Search completed. Finishing up.
> test-summariseOrphanCodes.R: v 1 candidate concept identified
> test-summariseOrphanCodes.R: Time taken: 0 minutes and 0 seconds
> test-summariseOrphanCodes.R: PHOEBE results not available
> test-summariseOrphanCodes.R: i The concept_recommended table is not present in the cdm.
> test-summariseOrphanCodes.R: Getting orphan codes for msk
> test-summariseOrphanCodes.R:
> test-summariseUnmappedCodes.R: Searching for unmapped codes related to cs
> test-summariseOrphanCodes.R: Getting orphan codes for msk
> test-summariseUnmappedCodes.R: - No unmapped codes found for cs
> test-summariseOrphanCodes.R:
> test-summariseUnmappedCodes.R: Searching for unmapped codes related to cs
> test-summariseOrphanCodes.R: Getting orphan codes for msk
> test-summariseUnmappedCodes.R: Searching for unmapped codes related to cs
> test-summariseOrphanCodes.R:
> test-summariseUnmappedCodes.R: - No unmapped codes found for cs
> test-tableUnmappedCodes.R: Searching for unmapped codes related to cs
Saving _problems/test-tableUnmappedCodes-50.R
Saving _problems/test-tableUnmappedCodes-51.R
Saving _problems/test-tableUnmappedCodes-52.R
Saving _problems/test-tableUnmappedCodes-55.R
[ FAIL 4 | WARN 576 | SKIP 26 | PASS 457 ]
══ Skipped tests (26) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-buildAchillesTables.R:2:3', 'test-drugCodes.R:141:3',
'test-drugCodes.R:461:3', 'test-getCandidateCodes.R:310:3',
'test-helperFunctions.R:2:3', 'test-helperFunctions.R:31:3',
'test-helperFunctions.R:46:3', 'test-helperFunctions.R:61:3',
'test-summariseCodeUse.R:2:3', 'test-summariseCodeUse.R:362:3',
'test-summariseCodeUse.R:810:3', 'test-summariseCodeUse.R:836:3',
'test-summariseCodeUse.R:869:3', 'test-tableAchillesCodeUse.R:2:3',
'test-tableAchillesCodeUse.R:66:3', 'test-tableCodeUse.R:2:3',
'test-tableCodeUse.R:85:3'
• Sys.getenv("CDM5_POSTGRESQL_DBNAME") == "" is TRUE (1): 'test-dbms.R:308:3'
• Sys.getenv("CDM5_REDSHIFT_DBNAME") == "" is TRUE (4):
'test-codesFrom.R:130:3', 'test-dbms.R:5:3', 'test-findUnmappedCodes.R:3:3',
'test-summariseCodeUse.R:555:3'
• Sys.getenv("CDM5_SQL_SERVER_SERVER") == "" is TRUE (2):
'test-codesInUse.R:39:3', 'test-dbms.R:460:3'
• Sys.getenv("SNOWFLAKE_SERVER") == "" is TRUE (1): 'test-dbms.R:170:3'
• Sys.getenv("darwinDbDatabaseServer") == "" is TRUE (1):
'test-synthea_sql_server.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-tableUnmappedCodes.R:50:3'): unmapped codes ──────────────────
Expected `tableUnmappedCodes(unmappedCodes)` not to throw any errors.
Actually got a <rlib_error_package_not_found> with message:
The package "visOmopResults" (>= 1.0.0) is required.
── Failure ('test-tableUnmappedCodes.R:51:3'): unmapped codes ──────────────────
Expected `tableUnmappedCodes(unmappedCodes, type = "tibble")` not to throw any errors.
Actually got a <rlib_error_package_not_found> with message:
The package "visOmopResults" (>= 1.0.0) is required.
── Failure ('test-tableUnmappedCodes.R:52:3'): unmapped codes ──────────────────
Expected `tableUnmappedCodes(unmappedCodes, header = NULL)` not to throw any errors.
Actually got a <rlib_error_package_not_found> with message:
The package "visOmopResults" (>= 1.0.0) is required.
── Failure ('test-tableUnmappedCodes.R:54:3'): unmapped codes ──────────────────
Expected `tableUnmappedCodes(omopgenerics::suppress(unmappedCodes))` not to throw any errors.
Actually got a <rlib_error_package_not_found> with message:
The package "visOmopResults" (>= 1.0.0) is required.
[ FAIL 4 | WARN 576 | SKIP 26 | PASS 457 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 3.5.0
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-gcc