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