Last updated on 2025-12-07 07:50:26 CET.
| Package | ERROR | WARN | NOTE | OK |
|---|---|---|---|---|
| CodelistGenerator | 1 | 12 | ||
| CohortConstructor | 1 | 1 | 2 | 9 |
| IncidencePrevalence | 1 | 12 | ||
| OmopOnSpark | 1 | 1 | 11 | |
| PhenotypeR | 1 | 3 | 9 |
Current CRAN status: ERROR: 1, OK: 12
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
Current CRAN status: ERROR: 1, WARN: 1, NOTE: 2, OK: 9
Version: 0.6.0
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'CirceR', 'covr', 'DiagrammeR', 'gt', 'knitr', 'rmarkdown',
'SqlRender', 'visOmopResults'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.6.0
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
Version: 0.6.0
Check: installed package size
Result: NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
doc 5.1Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-windows-x86_64
Version: 0.6.0
Check: package dependencies
Result: ERROR
Packages required and available but unsuitable versions:
'omopgenerics', 'PatientProfiles'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64
Current CRAN status: ERROR: 1, OK: 12
Version: 1.2.1
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'knitr', 'rmarkdown', 'Hmisc', 'spelling', 'gt', 'flextable',
'visOmopResults'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.1
Check: examples
Result: ERROR
Running examples in ‘IncidencePrevalence-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optionsTableIncidence
> ### Title: Additional arguments for the functions tableIncidence.
> ### Aliases: optionsTableIncidence
>
> ### ** Examples
>
> {
+ optionsTableIncidence()
+ }
Error in loadNamespace(x) : there is no package called ‘visOmopResults’
Calls: optionsTableIncidence ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [187s/113s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(IncidencePrevalence)
>
> test_check("IncidencePrevalence")
Starting 2 test processes.
> test-estimateIncidence.R: i Creating denominator cohorts
> test-estimatePrevalence.R: i Creating denominator cohorts
> test-estimateIncidence.R: v Cohorts created in 0 min and 4 sec
> test-estimateIncidence.R: i Getting incidence for analysis 1 of 1
> test-estimatePrevalence.R: v Cohorts created in 0 min and 10 sec
> test-estimatePrevalence.R: i Getting prevalence for analysis 1 of 1
> test-estimatePrevalence.R: v Time taken: 0 mins and 1 secs
> test-estimateIncidence.R: v Overall time taken: 0 mins and 3 secs
> test-estimateIncidence.R: i Getting incidence for analysis 1 of 1
> test-estimateIncidence.R: v Overall time taken: 0 mins and 3 secs
> test-estimatePrevalence.R: i Creating denominator cohorts
> test-estimateIncidence.R: i Creating denominator cohorts
> test-estimatePrevalence.R: v Cohorts created in 0 min and 4 sec
> test-estimatePrevalence.R: i Creating denominator cohorts
> test-estimateIncidence.R: v Cohorts created in 0 min and 4 sec
> test-estimateIncidence.R: i Creating denominator cohorts
> test-estimatePrevalence.R: v Cohorts created in 0 min and 4 sec
> test-estimateIncidence.R: -- getting cohort dates for ========>---------------------- 4 of 15 cohorts
> test-estimatePrevalence.R: i Creating denominator cohorts
> test-estimateIncidence.R: -- getting cohort dates for ====================>---------- 10 of 15 cohorts
> test-estimateIncidence.R: -- getting cohort dates for ==============================> 15 of 15 cohorts
> test-estimatePrevalence.R: v Cohorts created in 0 min and 5 sec
> test-estimatePrevalence.R: i Getting prevalence for analysis 1 of 1
> test-estimatePrevalence.R: v Time taken: 0 mins and 2 secs
> test-estimatePrevalence.R: i Getting prevalence for analysis 1 of 1
> test-estimateIncidence.R: v Cohorts created in 0 min and 15 sec
> test-estimateIncidence.R: i Getting incidence for analysis 1 of 1
> test-estimateIncidence.R: v Overall time taken: 0 mins and 2 secs
> test-estimatePrevalence.R: v Time taken: 0 mins and 4 secs
> test-estimatePrevalence.R: i Getting prevalence for analysis 1 of 1
> test-estimateIncidence.R: i Getting incidence for analysis 1 of 15
> test-estimateIncidence.R: i Getting incidence for analysis 2 of 15
> test-estimateIncidence.R: i Getting incidence for analysis 3 of 15
> test-estimateIncidence.R: i Getting incidence for analysis 4 of 15
> test-estimateIncidence.R: i Getting incidence for analysis 5 of 15
> test-estimateIncidence.R: i Getting incidence for analysis 6 of 15
> test-estimatePrevalence.R: v Time taken: 0 mins and 4 secs
> test-estimatePrevalence.R: i Getting prevalence for analysis 1 of 1
> test-estimateIncidence.R: i Getting incidence for analysis 7 of 15
> test-estimateIncidence.R: i Getting incidence for analysis 8 of 15
> test-estimateIncidence.R: i Getting incidence for analysis 9 of 15
> test-estimateIncidence.R: i Getting incidence for analysis 10 of 15
> test-estimateIncidence.R: i Getting incidence for analysis 11 of 15
> test-estimateIncidence.R: i Getting incidence for analysis 12 of 15
> test-estimateIncidence.R: i Getting incidence for analysis 13 of 15
> test-estimateIncidence.R: i Getting incidence for analysis 14 of 15
> test-estimateIncidence.R: i Getting incidence for analysis 15 of 15
> test-estimatePrevalence.R: v Time taken: 0 mins and 8 secs
> test-estimatePrevalence.R: i Getting prevalence for analysis 1 of 1
> test-estimateIncidence.R: v Overall time taken: 0 mins and 14 secs
Saving _problems/test-estimateIncidence-1056.R
> test-estimatePrevalence.R: v Time taken: 0 mins and 8 secs
> test-estimatePrevalence.R: i Getting prevalence for analysis 1 of 1
> test-estimatePrevalence.R: i Getting prevalence for analysis 1 of 1
> test-estimatePrevalence.R: i Getting prevalence for analysis 1 of 1
> test-generateDenominatorCohortSet.R: i Creating denominator cohorts
> test-generateDenominatorCohortSet.R: v Cohorts created in 0 min and 4 sec
> test-generateDenominatorCohortSet.R: i Creating denominator cohorts
> test-generateDenominatorCohortSet.R: v Cohorts created in 0 min and 7 sec
> test-generateDenominatorCohortSet.R: i Creating denominator cohorts
> test-generateDenominatorCohortSet.R: v Cohorts created in 0 min and 3 sec
> test-generateDenominatorCohortSet.R: i Creating denominator cohorts: target cohort id 1
> test-generateDenominatorCohortSet.R: v Cohorts created in 0 min and 5 sec
> test-generateDenominatorCohortSet.R: i Creating denominator cohorts: target cohort id 1
> test-generateDenominatorCohortSet.R: v Cohorts created in 0 min and 5 sec
[ FAIL 1 | WARN 0 | SKIP 101 | PASS 34 ]
══ Skipped tests (101) ═════════════════════════════════════════════════════════
• On CRAN (101): 'test-dateUtilities.R:2:3',
'test-benchmarkIncidencePrevalence.R:2:3',
'test-benchmarkIncidencePrevalence.R:45:3', 'test-estimateIncidence.R:57:3',
'test-estimateIncidence.R:120:3', 'test-estimateIncidence.R:230:3',
'test-estimateIncidence.R:300:3', 'test-estimateIncidence.R:399:3',
'test-estimateIncidence.R:503:3', 'test-estimateIncidence.R:598:3',
'test-estimateIncidence.R:762:3', 'test-estimateIncidence.R:869:3',
'test-estimateIncidence.R:1063:3', 'test-estimateIncidence.R:1127:3',
'test-estimateIncidence.R:1184:3', 'test-estimateIncidence.R:1269:3',
'test-estimateIncidence.R:1413:3', 'test-estimateIncidence.R:1529:3',
'test-estimateIncidence.R:1608:3', 'test-estimateIncidence.R:1716:3',
'test-estimateIncidence.R:1820:3', 'test-estimateIncidence.R:1979:3',
'test-estimateIncidence.R:2035:3', 'test-estimateIncidence.R:2233:3',
'test-estimateIncidence.R:2432:3', 'test-estimateIncidence.R:2517:3',
'test-estimateIncidence.R:2943:3', 'test-estimateIncidence.R:2991:3',
'test-estimateIncidence.R:3046:3', 'test-estimateIncidence.R:3104:3',
'test-estimateIncidence.R:3127:3', 'test-estimateIncidence.R:3142:3',
'test-estimateIncidence.R:3182:3', 'test-estimateIncidence.R:3344:3',
'test-estimateIncidence.R:3423:3', 'test-estimateIncidence.R:3467:3',
'test-estimateIncidence.R:3513:3', 'test-estimateIncidence.R:3561:3',
'test-estimatePrevalence.R:41:3', 'test-estimatePrevalence.R:93:3',
'test-estimatePrevalence.R:150:3', 'test-estimatePrevalence.R:269:3',
'test-estimatePrevalence.R:413:3', 'test-estimatePrevalence.R:495:3',
'test-estimatePrevalence.R:646:3', 'test-estimatePrevalence.R:697:3',
'test-estimatePrevalence.R:742:3', 'test-estimatePrevalence.R:797:3',
'test-estimatePrevalence.R:845:3', 'test-estimatePrevalence.R:869:3',
'test-estimatePrevalence.R:894:3', 'test-estimatePrevalence.R:1035:3',
'test-estimatePrevalence.R:1082:3', 'test-estimatePrevalence.R:1115:3',
'test-estimatePrevalence.R:1194:3', 'test-estimatePrevalence.R:1246:3',
'test-estimatePrevalence.R:1416:3', 'test-estimatePrevalence.R:1458:3',
'test-estimatePrevalence.R:1504:3', 'test-estimatePrevalence.R:1556:3',
'test-estimatePrevalence.R:1672:3', 'test-getStudyDays.R:2:3',
'test-getStudyDays.R:238:3', 'test-mockIncidencePrevalence.R:2:3',
'test-mockIncidencePrevalence.R:39:3', 'test-mockIncidencePrevalence.R:69:3',
'test-mockIncidencePrevalence.R:171:3', 'test-plotting.R:2:3',
'test-plotting.R:203:3', 'test-plotting.R:252:3', 'test-plotting.R:302:3',
'test-plotting.R:366:3', 'test-tables.R:2:3', 'test-tables.R:126:3',
'test-tidyResults.R:2:3', 'test-tidyResults.R:57:3',
'test-generateDenominatorCohortSet.R:138:3',
'test-generateDenominatorCohortSet.R:185:3',
'test-generateDenominatorCohortSet.R:289:3',
'test-generateDenominatorCohortSet.R:326:3',
'test-generateDenominatorCohortSet.R:591:3',
'test-generateDenominatorCohortSet.R:641:3',
'test-generateDenominatorCohortSet.R:720:3',
'test-generateDenominatorCohortSet.R:812:3',
'test-generateDenominatorCohortSet.R:855:3',
'test-generateDenominatorCohortSet.R:907:3',
'test-generateDenominatorCohortSet.R:991:3',
'test-generateDenominatorCohortSet.R:1118:3',
'test-generateDenominatorCohortSet.R:1199:3',
'test-generateDenominatorCohortSet.R:1263:3',
'test-generateDenominatorCohortSet.R:1316:3',
'test-generateDenominatorCohortSet.R:1374:3',
'test-generateDenominatorCohortSet.R:1449:3',
'test-generateDenominatorCohortSet.R:1572:3',
'test-generateDenominatorCohortSet.R:1673:3',
'test-generateDenominatorCohortSet.R:1726:3',
'test-generateDenominatorCohortSet.R:1789:3',
'test-generateDenominatorCohortSet.R:2018:3',
'test-generateDenominatorCohortSet.R:2109:3',
'test-generateDenominatorCohortSet.R:2309:3',
'test-generateDenominatorCohortSet.R:2413:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-estimateIncidence.R:1049:3'): mock db: multiple denominator inputs ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `tableIncidence(inc_1, type = "tibble")`: The package "visOmopResults" (>= 1.0.2) is required.
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-estimateIncidence.R:1049:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─IncidencePrevalence::tableIncidence(inc_1, type = "tibble")
5. └─rlang::check_installed("visOmopResults", version = "1.0.2")
[ FAIL 1 | WARN 0 | SKIP 101 | PASS 34 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.1
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
Current CRAN status: ERROR: 1, WARN: 1, OK: 11
Version: 0.1.0
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'knitr', 'rmarkdown', 'sparklyr', 'DatabaseConnector'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
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
Version: 0.1.0
Check: package dependencies
Result: ERROR
Package required and available but unsuitable version: ‘omopgenerics’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64
Current CRAN status: WARN: 1, NOTE: 3, OK: 9
Version: 0.2.0
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'gt', 'knitr', 'DiagrammeR', 'reactable', 'reactablefmtr',
'sortable', 'DT', 'plotly', 'usethis', 'rmarkdown', 'visOmopResults',
'rsconnect'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.0
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
Version: 0.2.0
Check: installed package size
Result: NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
doc 4.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64