* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/CohortCharacteristics.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 ‘CohortCharacteristics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CohortCharacteristics’ version ‘0.1.0’
* 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 ‘CohortCharacteristics’ can be installed ... [13s/34s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/CohortCharacteristics-00install.html' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... 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 ... [27s/89s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [115s/118s] ERROR
  Running ‘spelling.R’
  Running ‘testthat.R’ [114s/116s]
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(CohortCharacteristics)
  > 
  > test_check("CohortCharacteristics")
  Starting 2 test processes
  [ FAIL 5 | WARN 0 | SKIP 13 | PASS 5 ]
  
  ══ Skipped tests (13) ══════════════════════════════════════════════════════════
  • On CRAN (12): 'test-plotCharacteristics.R:2:3',
    'test-plotLargeScaleCharacteristics.R:3:3', 'test-plotSummarised.R:2:3',
    'test-plotSummarised.R:82:3', 'test-plotSummarised.R:179:3',
    'test-plotSummarised.R:263:3', 'test-summariseCohortIntersect.R:2:3',
    'test-summariseCohortOverlap.R:2:3', 'test-summariseCohortTiming.R:2:3',
    'test-summariseLargeScaleCharacteristics.R:2:3',
    'test-tableSummarised.R:2:3', 'test-tableSummarised.R:114:3'
  • empty test (1): 'test-tableSummarised.R:235:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-summariseCharacteristics.R:76:3'): test summariseCharacteristics ──
  Expected `... <- NULL` 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.
  ── Error ('test-summariseCharacteristics.R:88:3'): test summariseCharacteristics ──
  Error in `eval(code, test_env)`: object 'result' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_true(inherits(result, "summarised_result")) at test-summariseCharacteristics.R:88:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::inherits(result, "summarised_result")
  ── Failure ('test-summariseCharacteristics.R:291:3'): test empty cohort ────────
  Expected `summariseCharacteristics(...)` 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-summariseCharacteristics.R:301:3'): test empty cohort ────────
  Expected `... <- NULL` 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-summariseCharacteristics.R:308:3'): test empty cohort ────────
  Expected `... <- NULL` 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 5 | WARN 0 | SKIP 13 | PASS 5 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [60s/115s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘a06_summarisePatientCharacteristics.Rmd’ using rmarkdown

Quitting from lines  at lines 27-109 [unnamed-chunk-2] (a06_summarisePatientCharacteristics.Rmd)
Error: processing vignette 'a06_summarisePatientCharacteristics.Rmd' failed with diagnostics:
Can't select columns that don't exist.
✖ Column `result_type` doesn't exist.
--- failed re-building ‘a06_summarisePatientCharacteristics.Rmd’

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a08_summariseCohortOverlap.Rmd’ using rmarkdown
--- finished re-building ‘a08_summariseCohortOverlap.Rmd’

SUMMARY: processing the following file failed:
  ‘a06_summarisePatientCharacteristics.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... 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: 2 ERRORs