* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/DrugUtilisation.Rcheck’
* using R Under development (unstable) (2024-05-02 r86508)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 18.1.5
    flang-new version 18.1.5
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘DrugUtilisation/DESCRIPTION’ ... OK
* this is package ‘DrugUtilisation’ version ‘0.5.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DrugUtilisation’ can be installed ... [16s/35s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/DrugUtilisation-00install.html' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... [3s/11s] OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [25s/79s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [546s/292s] ERROR
  Running ‘testthat.R’ [546s/291s]
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(DrugUtilisation)
  > 
  > test_check("DrugUtilisation")
  Starting 2 test processes
  [ FAIL 3 | WARN 71 | SKIP 20 | PASS 154 ]
  
  ══ Skipped tests (20) ══════════════════════════════════════════════════════════
  • On CRAN (19): 'test-benchmarkDUS.R:2:3', 'test-dailyDose.R:2:3',
    'test-generateDrugUtilisationCohortSet.R:48:3',
    'test-generateDrugUtilisationCohortSet.R:147:3',
    'test-generateDrugUtilisationCohortSet.R:203:3',
    'test-generateDrugUtilisationCohortSet.R:253:3',
    'test-generateDrugUtilisationCohortSet.R:349:3', 'test-drugUse.R:2:3',
    'test-drugUse.R:40:3', 'test-drugUse.R:254:3', 'test-drugUse.R:455:3',
    'test-drugUse.R:597:3', 'test-drugUse.R:847:3', 'test-drugUse.R:868:3',
    'test-drugUse.R:914:3', 'test-indication.R:3:3', 'test-indication.R:185:3',
    'test-indication.R:339:3', 'test-indication.R:464:3'
  • empty test (1): 'test-generateConceptCohortSet.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-indication.R:648:3'): summariseIndication ────────────────────
  grepl("summarised_indication", unique(result$result_type)) is not TRUE
  
  `actual`:       
  `expected`: TRUE
  ── Failure ('test-largeScaleCharacteristics.R:8:3'): basic functionality summariseCodelist ──
  Expected `summariseCharacteristicsFromCodelist(cdm[["cohort1"]], conceptSet = conceptSet)` to run without any errors.
  i Actually got a <vctrs_error_subscript_oob> with text:
    Can't select columns that don't exist.
    x Column `result_type` doesn't exist.
  ── Failure ('test-largeScaleCharacteristics.R:14:3'): basic functionality summariseCodelist ──
  Expected `summariseCharacteristicsFromCodelist(...)` to run without any errors.
  i Actually got a <vctrs_error_subscript_oob> with text:
    Can't select columns that don't exist.
    x Column `result_type` doesn't exist.
  
  [ FAIL 3 | WARN 71 | SKIP 20 | PASS 154 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... [8s/10s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR