Running ‘testthat.R’ [152s/248s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(CodelistGenerator)
  > 
  > test_check("CodelistGenerator")
  -- keywords: arthritis
  -- domains: Condition
  -- conceptClassId: 
  -- vocabularyId: 
  -- exactMatch: FALSE
  -- standardConcept: Standard
  -- searchInSynonyms: FALSE
  -- searchViaSynonyms: FALSE
  -- searchNonStandard: FALSE
  -- fuzzyMatch: FALSE
  -- maxDistanceCost: 0.1
  -- exclude: 
  -- includeDescendants: TRUE
  -- includeAncestor: FALSE
  Checking inputs
  Starting search
  condition: Limiting to potential concepts of interest
  condition: Getting concepts to include
  condition: Getting concepts to include from descendants
  Time: 0 minutes and 3 seconds
  Search strategy
  -- keywords: arthritis
  -- domains: Condition
  -- conceptClassId: Clinical Finding
  -- vocabularyId: 
  -- exactMatch: FALSE
  -- standardConcept: Standard
  -- searchInSynonyms: TRUE
  -- searchViaSynonyms: TRUE
  -- searchNonStandard: TRUE
  -- fuzzyMatch: FALSE
  -- maxDistanceCost: 0.1
  -- exclude: Childhood asthma
  -- includeDescendants: TRUE
  -- includeAncestor: TRUE
  Checking inputs
  Starting search
  condition: Limiting to potential concepts of interest
  condition: Getting concepts to exclude
  condition: Getting concepts to include
  condition: Getting from exact matches of synonyms
  condition: Getting concepts to include from descendants
  condition: Getting concepts to include from direct ancestors of identified concepts
  condition: Getting concepts to include from non-standard concepts
  Time: 0 minutes and 5 seconds
  Search strategy
  -- keywords: Arthritis
  -- domains: Condition
  -- conceptClassId: Clinical Finding
  -- vocabularyId: 
  -- exactMatch: FALSE
  -- standardConcept: Standard
  -- searchInSynonyms: TRUE
  -- searchViaSynonyms: TRUE
  -- searchNonStandard: TRUE
  -- fuzzyMatch: TRUE
  -- maxDistanceCost: 0.1
  -- exclude: Osteoarthritis of hip
  -- includeDescendants: TRUE
  -- includeAncestor: TRUE
  Checking inputs
  Starting search
  condition: Limiting to potential concepts of interest
  condition: Getting concepts to exclude
  condition: Getting concepts to include
  condition: Getting from exact matches of synonyms
  condition: Getting concepts to include from descendants
  condition: Getting concepts to include from direct ancestors of identified concepts
  condition: Getting concepts to include from non-standard concepts
  Time: 0 minutes and 6 seconds
  -- No codes found for given search strategy
  -- No codes found for given search strategy
  -- No codes found for given search strategy
  -- No codes found for given search strategy
  -- No codes found for given search strategy
  -- keywords: arthritis
  -- domains: Condition
  -- conceptClassId: 
  -- vocabularyId: 
  -- exactMatch: FALSE
  -- standardConcept: Standard
  -- searchInSynonyms: FALSE
  -- searchViaSynonyms: FALSE
  -- searchNonStandard: FALSE
  -- fuzzyMatch: FALSE
  -- maxDistanceCost: 0.1
  -- exclude: 
  -- includeDescendants: TRUE
  -- includeAncestor: FALSE
  Checking inputs
  Starting search
  condition: Limiting to potential concepts of interest
  condition: Getting concepts to include
  condition: Getting concepts to include from descendants
  Time: 0 minutes and 0 seconds
  Search strategy
  -- keywords: arthritis
  -- domains: Condition
  -- conceptClassId: Clinical Finding
  -- vocabularyId: 
  -- exactMatch: FALSE
  -- standardConcept: Standard
  -- searchInSynonyms: TRUE
  -- searchViaSynonyms: TRUE
  -- searchNonStandard: TRUE
  -- fuzzyMatch: FALSE
  -- maxDistanceCost: 0.1
  -- exclude: Childhood asthma
  -- includeDescendants: TRUE
  -- includeAncestor: TRUE
  Checking inputs
  Starting search
  condition: Limiting to potential concepts of interest
  condition: Getting concepts to exclude
  condition: Getting concepts to include
  condition: Getting from exact matches of synonyms
  condition: Getting concepts to include from descendants
  condition: Getting concepts to include from direct ancestors of identified concepts
  condition: Getting concepts to include from non-standard concepts
  Time: 0 minutes and 0 seconds
  Search strategy
  -- keywords: Arthritis
  -- domains: Condition
  -- conceptClassId: Clinical Finding
  -- vocabularyId: 
  -- exactMatch: FALSE
  -- standardConcept: Standard
  -- searchInSynonyms: TRUE
  -- searchViaSynonyms: TRUE
  -- searchNonStandard: TRUE
  -- fuzzyMatch: TRUE
  -- maxDistanceCost: 0.1
  -- exclude: Osteoarthritis of hip
  -- includeDescendants: TRUE
  -- includeAncestor: TRUE
  Checking inputs
  Starting search
  condition: Limiting to potential concepts of interest
  condition: Getting concepts to exclude
  condition: Getting concepts to include
  condition: Getting from exact matches of synonyms
  condition: Getting concepts to include from descendants
  condition: Getting concepts to include from direct ancestors of identified concepts
  condition: Getting concepts to include from non-standard concepts
  Time: 0 minutes and 0 seconds
  -- No codes found for given search strategy
  -- No codes found for given search strategy
  -- No codes found for given search strategy
  -- No codes found for given search strategy
  -- No codes found for given search strategy
  -- No codes found for given search strategy
  -- No codes found for given search strategy
  -- No codes found --
  
  i No ICD-10 chapter codes were found in the concept table.
  -- Were ICD-10 codes included when loading vocabularies into the database?
  [ FAIL 0 | WARN 127 | SKIP 5 | PASS 219 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • Sys.getenv("CDM5_REDSHIFT_DBNAME") == "" is TRUE (4):
    'test-summariseCodeUse.R:3:3', 'test-summariseCodeUse.R:154:3',
    'test-summariseCodeUse.R:184:3', 'test-summariseCodeUse.R:240:3'
  • Sys.getenv("darwinDbDatabaseServer") == "" is TRUE (1):
    'test-synthea_sql_server.R:2:3'
  
  [ FAIL 0 | WARN 127 | SKIP 5 | PASS 219 ]
  > 
  > proc.time()
     user  system elapsed 
  149.764   1.867 247.315 
  Error: bad value
  Execution halted