* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/clinDataReview.Rcheck’
* using R Under development (unstable) (2025-02-21 r87787)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘clinDataReview/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clinDataReview’ version ‘1.6.1’
* 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 ‘clinDataReview’ can be installed ... [20s/24s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/clinDataReview-00install.html' for details.
* 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 whether startup messages can be suppressed ... 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 ... [29s/29s] 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 ... [23s/23s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [57s/58s] ERROR
  Running ‘testthat.R’ [57s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clinDataReview)
  > 
  > test_check("clinDataReview")
    adding: report.html (deflated 63%)
    adding: report_dependencies1b286d153cdf5a/ (stored 0%)
    adding: report_dependencies1b286d153cdf5a/file1b286d31d59e32.html (deflated 8%)
  [ FAIL 6 | WARN 0 | SKIP 31 | PASS 509 ]
  
  ══ Skipped tests (31) ══════════════════════════════════════════════════════════
  • On CRAN (31): 'test_knitPrint.R:35:2', 'test_knitPrint.R:76:2',
    'test_knitPrint.R:129:2', 'test_knitPrint.R:182:2', 'test_knitPrint.R:228:2',
    'test_knitPrint.R:290:2', 'test_render_clinDataReviewReport.R:371:2',
    'test_render_clinDataReviewReport.R:414:2',
    'test_render_clinDataReviewReport.R:452:2',
    'test_render_clinDataReviewReport.R:497:2',
    'test_render_clinDataReviewReport.R:561:2',
    'test_render_clinDataReviewReport.R:633:2',
    'test_render_clinDataReviewReport.R:700:2',
    'test_render_clinDataReviewReport.R:758:2',
    'test_render_clinDataReviewReport.R:816:2',
    'test_render_clinDataReviewReport.R:874:2',
    'test_render_clinDataReviewReport.R:1048:2',
    'test_render_clinDataReviewReport.R:1119:3',
    'test_render_clinDataReviewReport.R:1230:2',
    'test_render_clinDataReviewReport.R:1371:3',
    'test_render_clinDataReviewReport.R:1489:3', 'test_skeleton.R:92:2',
    'test_skeleton.R:132:3', 'test_templates.R:53:2', 'test_templates.R:100:3',
    'test_templates.R:162:2', 'test_templates.R:208:2', 'test_templates.R:255:2',
    'test_templates.R:306:3', 'test_templates.R:369:2', 'test_templates.R:418:2'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_annotateData.R:207:2'): Data is correctly annotated based on an exported dataset ──
  Error in `tempdir(check)`: NA in coercion to Rboolean
  Backtrace:
      â–†
   1. └─base::tempdir("annotation") at test_annotateData.R:207:9
  ── Error ('test_annotateData.R:237:2'): Data is correctly annotated with a specified variable based on an exported dataset ──
  Error in `tempdir(check)`: NA in coercion to Rboolean
  Backtrace:
      â–†
   1. └─base::tempdir("annotation") at test_annotateData.R:237:9
  ── Error ('test_annotateData.R:371:2'): Data is correctly annotated based on the preset 'demographics' option ──
  Error in `tempdir(check)`: NA in coercion to Rboolean
  Backtrace:
      â–†
   1. └─base::tempdir("annotation") at test_annotateData.R:371:9
  ── Error ('test_annotateData.R:456:2'): Data is correctly annotated based on the preset 'exposed_subjects' option ──
  Error in `tempdir(check)`: NA in coercion to Rboolean
  Backtrace:
      â–†
   1. └─base::tempdir("annotation") at test_annotateData.R:456:9
  ── Error ('test_annotateData.R:490:2'): An error is generated when annotating with the preset 'exposed_subjects' option, but this dataset does not contain a subject variable ──
  Error in `tempdir(check)`: NA in coercion to Rboolean
  Backtrace:
      â–†
   1. └─base::tempdir("annotation") at test_annotateData.R:490:9
  ── Error ('test_annotateData.R:515:2'): An error is generated when annotating with the preset 'exposed_subjects' option, but this dataset does not contain a start time variable ──
  Error in `tempdir(check)`: NA in coercion to Rboolean
  Backtrace:
      â–†
   1. └─base::tempdir("annotation") at test_annotateData.R:515:9
  
  [ FAIL 6 | WARN 0 | SKIP 31 | PASS 509 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [44s/44s] OK
* checking PDF version of manual ... [12s/12s] 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