Package: CodelistGenerator
Check: tests
New result: ERROR
    Running ‘testthat.R’ [229s/123s]
  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