Running ‘testthat.R’ [60s/44s]
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
  [ FAIL 18 | WARN 0 | SKIP 8 | PASS 3 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-summariseCodeUse.R:2:1', 'test-summariseCodeUse.R:290:3'
  • Sys.getenv("CDM5_REDSHIFT_DBNAME") == "" is TRUE (4):
    'test-codesFrom.R:100:3', 'test-dbms.R:6:3', 'test-findUnmappedCodes.R:3:3',
    'test-summariseCodeUse.R:498:3'
  • Sys.getenv("CDM5_SQL_SERVER_SERVER") == "" is TRUE (1):
    'test-codesInUse.R:36:3'
  • Sys.getenv("darwinDbDatabaseServer") == "" is TRUE (1):
    'test-synthea_sql_server.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-achillesCodeUse.R:4:3'): achilles code use ─────────────────────
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef("database") at test-achillesCodeUse.R:4:3
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-codesFrom.R:6:5'): test inputs - mock ──────────────────────────
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-codesFrom.R:6:5
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-codesInUse.R:4:3'): tests with mock db ─────────────────────────
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef("database") at test-codesInUse.R:4:3
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-compareCodelists.R:6:5'): comparing two codelists ──────────────
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-compareCodelists.R:6:5
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-compareCodelists.R:77:5'): comparing two codelists- same codes found different ways ──
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-compareCodelists.R:77:5
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-findOrphanCodes.R:4:5'): tests with mock db ────────────────────
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef("database") at test-findOrphanCodes.R:4:5
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-drugCodes.R:5:3'): getATCCodes working ─────────────────────────
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backend = backends[i]) at test-drugCodes.R:5:3
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-drugCodes.R:33:5'): getATCCodes expected errors ────────────────
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backend = backends[i]) at test-drugCodes.R:33:5
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-drugCodes.R:49:5'): getDrugIngredientCodes working ─────────────
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backend = backends[i]) at test-drugCodes.R:49:5
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-drugCodes.R:111:5'): getDrugIngredientCodes expected errors ────
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backend = backends[i]) at test-drugCodes.R:111:5
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-getCandidateCodes.R:7:5'): tests with mock db ──────────────────
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-getCandidateCodes.R:7:5
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-getCandidateCodes.R:269:5'): tests with mock db - multiple domains ──
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-getCandidateCodes.R:269:5
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-getMappings.R:6:5'): tests with mock ───────────────────────────
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-getMappings.R:6:5
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-mockVocabRef.R:2:3'): mock vocab db ────────────────────────────
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef("database") at test-mockVocabRef.R:2:3
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-getICD10StandardCodes.R:4:5'): db without icd10 codes loaded ───
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backend = backends[i]) at test-getICD10StandardCodes.R:4:5
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-getICD10StandardCodes.R:59:3'): db without icd10 codes loaded ──
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef() at test-getICD10StandardCodes.R:59:3
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-getICD10StandardCodes.R:68:3'): expected errors ────────────────
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef() at test-getICD10StandardCodes.R:68:3
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  ── Error ('test-vocabUtilities.R:6:5'): tests with mock db ─────────────────────
  Error in `newAchillesTable(value)`: stratum_1_name, stratum_2_name, stratum_3_name, stratum_4_name, stratum_5_name, is_default and category are not present in table achilles_analysis
  Backtrace:
      ▆
   1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-vocabUtilities.R:6:5
   2.   ├─base::`$<-`(`*tmp*`, "achilles_analysis", value = `<tbl_dck_[,2]>`)
   3.   └─omopgenerics:::`$<-.cdm_reference`(...)
   4.     ├─base::`[[<-`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   5.     └─omopgenerics:::`[[<-.cdm_reference`(`*tmp*`, name, value = `<tbl_dck_[,2]>`)
   6.       └─omopgenerics::newAchillesTable(value)
   7.         └─omopgenerics:::checkColumnsCdm(table, name, cols)
   8.           └─cli::cli_abort(...)
   9.             └─rlang::abort(...)
  
  [ FAIL 18 | WARN 0 | SKIP 8 | PASS 3 ]
  Error: Test failures
  Execution halted