Running ‘testthat.R’ [14s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(CodelistGenerator)
  > 
  > test_check("CodelistGenerator")
  [ FAIL 15 | WARN 0 | SKIP 5 | PASS 3 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Sys.getenv("CDM5_REDSHIFT_DBNAME") == "" is TRUE (4)
  • Sys.getenv("darwinDbDatabaseServer") == "" is TRUE (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-compareCodelists.R:6:5'): comparing two codelists ──────────────
  Error in `CDMConnector::cdm_from_con(db, cdm_tables = tidyselect::all_of(c("concept", 
      "concept_relationship", "concept_ancestor", "concept_synonym", 
      "vocabulary", "drug_strength")))`: unused argument (cdm_tables = tidyselect::all_of(c("concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary", "drug_strength")))
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-compareCodelists.R:6:4
  ── Error ('test-compareCodelists.R:77:5'): comparing two codelists- same codes found different ways ──
  Error in `CDMConnector::cdm_from_con(db, cdm_tables = tidyselect::all_of(c("concept", 
      "concept_relationship", "concept_ancestor", "concept_synonym", 
      "vocabulary", "drug_strength")))`: unused argument (cdm_tables = tidyselect::all_of(c("concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary", "drug_strength")))
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-compareCodelists.R:77:4
  ── Error ('test-drugCodes.R:5:3'): getATCCodes working ─────────────────────────
  Error in `CDMConnector::cdm_from_con(db, cdm_tables = tidyselect::all_of(c("concept", 
      "concept_relationship", "concept_ancestor", "concept_synonym", 
      "vocabulary", "drug_strength")))`: unused argument (cdm_tables = tidyselect::all_of(c("concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary", "drug_strength")))
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backend = backends[i]) at test-drugCodes.R:5:2
  ── Error ('test-drugCodes.R:25:5'): getATCCodes expected errors ────────────────
  Error in `CDMConnector::cdm_from_con(db, cdm_tables = tidyselect::all_of(c("concept", 
      "concept_relationship", "concept_ancestor", "concept_synonym", 
      "vocabulary", "drug_strength")))`: unused argument (cdm_tables = tidyselect::all_of(c("concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary", "drug_strength")))
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backend = backends[i]) at test-drugCodes.R:25:4
  ── Error ('test-drugCodes.R:41:5'): getDrugIngredientCodes working ─────────────
  Error in `CDMConnector::cdm_from_con(db, cdm_tables = tidyselect::all_of(c("concept", 
      "concept_relationship", "concept_ancestor", "concept_synonym", 
      "vocabulary", "drug_strength")))`: unused argument (cdm_tables = tidyselect::all_of(c("concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary", "drug_strength")))
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backend = backends[i]) at test-drugCodes.R:41:4
  ── Error ('test-drugCodes.R:69:5'): getDrugIngredientCodes expected errors ─────
  Error in `CDMConnector::cdm_from_con(db, cdm_tables = tidyselect::all_of(c("concept", 
      "concept_relationship", "concept_ancestor", "concept_synonym", 
      "vocabulary", "drug_strength")))`: unused argument (cdm_tables = tidyselect::all_of(c("concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary", "drug_strength")))
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backend = backends[i]) at test-drugCodes.R:69:4
  ── Error ('test-getCandidateCodes.R:6:5'): tests with mock db ──────────────────
  Error in `CDMConnector::cdm_from_con(db, cdm_tables = tidyselect::all_of(c("concept", 
      "concept_relationship", "concept_ancestor", "concept_synonym", 
      "vocabulary", "drug_strength")))`: unused argument (cdm_tables = tidyselect::all_of(c("concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary", "drug_strength")))
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-getCandidateCodes.R:6:4
  ── Error ('test-getCandidateCodes.R:403:5'): tests with mock db - multiple domains ──
  Error in `CDMConnector::cdm_from_con(db, cdm_tables = tidyselect::all_of(c("concept", 
      "concept_relationship", "concept_ancestor", "concept_synonym", 
      "vocabulary", "drug_strength")))`: unused argument (cdm_tables = tidyselect::all_of(c("concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary", "drug_strength")))
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-getCandidateCodes.R:403:4
  ── Error ('test-getCandidateCodes.R:437:5'): tests exact match ─────────────────
  Error in `CDMConnector::cdm_from_con(db, cdm_tables = tidyselect::all_of(c("concept", 
      "concept_relationship", "concept_ancestor", "concept_synonym", 
      "vocabulary", "drug_strength")))`: unused argument (cdm_tables = tidyselect::all_of(c("concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary", "drug_strength")))
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-getCandidateCodes.R:437:4
  ── Error ('test-getICD10StandardCodes.R:2:3'): db without icd10 codes loaded ───
  Error in `CDMConnector::cdm_from_con(db, cdm_tables = tidyselect::all_of(c("concept", 
      "concept_relationship", "concept_ancestor", "concept_synonym", 
      "vocabulary", "drug_strength")))`: unused argument (cdm_tables = tidyselect::all_of(c("concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary", "drug_strength")))
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef() at test-getICD10StandardCodes.R:2:2
  ── Error ('test-getICD10StandardCodes.R:23:3'): db without icd10 codes loaded ──
  Error in `CDMConnector::cdm_from_con(db, cdm_tables = tidyselect::all_of(c("concept", 
      "concept_relationship", "concept_ancestor", "concept_synonym", 
      "vocabulary", "drug_strength")))`: unused argument (cdm_tables = tidyselect::all_of(c("concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary", "drug_strength")))
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef() at test-getICD10StandardCodes.R:23:2
  ── Error ('test-getICD10StandardCodes.R:32:3'): expected errors ────────────────
  Error in `CDMConnector::cdm_from_con(db, cdm_tables = tidyselect::all_of(c("concept", 
      "concept_relationship", "concept_ancestor", "concept_synonym", 
      "vocabulary", "drug_strength")))`: unused argument (cdm_tables = tidyselect::all_of(c("concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary", "drug_strength")))
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef() at test-getICD10StandardCodes.R:32:2
  ── Error ('test-getMappings.R:6:5'): tests with mock ───────────────────────────
  Error in `CDMConnector::cdm_from_con(db, cdm_tables = tidyselect::all_of(c("concept", 
      "concept_relationship", "concept_ancestor", "concept_synonym", 
      "vocabulary", "drug_strength")))`: unused argument (cdm_tables = tidyselect::all_of(c("concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary", "drug_strength")))
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-getMappings.R:6:4
  ── Error ('test-mockVocabRef.R:2:3'): mock vocab db ────────────────────────────
  Error in `CDMConnector::cdm_from_con(db, cdm_tables = tidyselect::all_of(c("concept", 
      "concept_relationship", "concept_ancestor", "concept_synonym", 
      "vocabulary", "drug_strength")))`: unused argument (cdm_tables = tidyselect::all_of(c("concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary", "drug_strength")))
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef("database") at test-mockVocabRef.R:2:2
  ── Error ('test-vocabUtilities.R:6:5'): tests with mock db ─────────────────────
  Error in `CDMConnector::cdm_from_con(db, cdm_tables = tidyselect::all_of(c("concept", 
      "concept_relationship", "concept_ancestor", "concept_synonym", 
      "vocabulary", "drug_strength")))`: unused argument (cdm_tables = tidyselect::all_of(c("concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary", "drug_strength")))
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-vocabUtilities.R:6:4
  
  [ FAIL 15 | WARN 0 | SKIP 5 | PASS 3 ]
  Error: Test failures
  In addition: Warning messages:
  1: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  2: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  3: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  4: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  5: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  Execution halted
  There were 25 warnings (use warnings() to see them)