Running ‘testthat.R’ [281s/193s]
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 15 | WARN 754 | SKIP 14 | PASS 399 ]
  
  ══ Skipped tests (14) ══════════════════════════════════════════════════════════
  • On CRAN (6): 'test-drugCodes.R:123:3', 'test-drugCodes.R:435:3',
    'test-getICD10StandardCodes.R:84:3', 'test-getCandidateCodes.R:310:3',
    'test-summariseCodeUse.R:2:1', 'test-summariseCodeUse.R:295:3'
  • Sys.getenv("CDM5_POSTGRESQL_DBNAME") == "" is TRUE (1): 'test-dbms.R:292:3'
  • Sys.getenv("CDM5_REDSHIFT_DBNAME") == "" is TRUE (4):
    'test-codesFrom.R:131:3', 'test-dbms.R:5:3', 'test-findUnmappedCodes.R:3:3',
    'test-summariseCodeUse.R:492:3'
  • Sys.getenv("CDM5_SQL_SERVER_SERVER") == "" is TRUE (1):
    'test-codesInUse.R:36:3'
  • Sys.getenv("SNOWFLAKE_SERVER") == "" is TRUE (1): 'test-dbms.R:154:3'
  • Sys.getenv("darwinDbDatabaseServer") == "" is TRUE (1):
    'test-synthea_sql_server.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-tableAchillesCodeUse.R:20:3'): table achilles code use expcted columns ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-tableAchillesCodeUse.R:66:3'): table achilles code use expcted columns ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-tableAchillesCodeUse.R:80:3'): table achilles code use expcted columns ──
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-tableCodeUse.R:39:3'): table code use expcted columns ────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-tableCodeUse.R:55:3'): table code use expcted columns ────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-tableCodeUse.R:71:3'): table code use expcted columns ────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-tableCodeUse.R:87:3'): table code use expcted columns ────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-tableCodeUse.R:118:3'): table code use expcted columns ───────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-tableCodeUse.R:136:3'): table code use expcted columns ───────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-tableCodeUse.R:141:3'): table code use expcted columns ───────
  levels(tab6$body$dataset$group) == "Pharyngitis; Cs" is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Error ('test-tableCodeUse.R:144:3'): table code use expcted columns ─────────
  Error in `checkColumnsFormat(x = x, "summarised_result")`: The following colum does not have a correct format
  * NA: format=character (expected=NA)
  Backtrace:
      ▆
   1. └─CodelistGenerator::tableCohortCodeUse(...) at test-tableCodeUse.R:144:3
   2.   └─CodelistGenerator:::internalTableCodeUse(...)
   3.     └─visOmopResults::visOmopTable(...)
   4.       └─omopgenerics::validateResultArguemnt(result)
   5.         └─omopgenerics::validateResultArgument(...)
   6.           └─omopgenerics:::validateSummariseResult(result)
   7.             └─omopgenerics:::checkColumnsFormat(x = x, "summarised_result")
   8.               └─cli::cli_abort(...)
   9.                 └─rlang::abort(...)
  ── Failure ('test-tableCodeUse.R:272:3'): table code use output formats ────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-tableCodeUse.R:273:3'): table code use output formats ────────
  as.character(tab1$body$dataset$`Codelist name`[1:3]) (`actual`) not equal to c("Acetiminophen", NA, NA) (`expected`).
  
  `actual`:   "acetiminophen" NA NA
  `expected`: "Acetiminophen" NA NA
  ── Failure ('test-tableCodeUse.R:307:3'): table code use output formats ────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-tableCodeUse.R:342:3'): tableCodeUse expected behaviour ──────
  `tableCodeUse(...)` did not throw the expected error.
  
  [ FAIL 15 | WARN 754 | SKIP 14 | PASS 399 ]
  Error: Test failures
  Execution halted