* using log directory ‘/data/gannet/ripley/R/packages/tests-noLD/VizTest.Rcheck’
* using R Under development (unstable) (2025-12-07 r89119)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
    GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘VizTest/DESCRIPTION’ ... OK
* this is package ‘VizTest’ version ‘0.6’
* 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 ‘VizTest’ can be installed ... [21s/93s] 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 ... [6s/21s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/19s] OK
* checking whether the package can be unloaded cleanly ... [5s/18s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/19s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/19s] OK
* checking loading without being on the library search path ... [6s/27s] 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 ... [30s/119s] 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 ... [9s/42s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [12s/48s]
 [12s/51s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [21m/66m] ERROR
Error(s) in re-building vignettes:
--- re-building ‘compact_letter_displays.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘compact_letter_displays.Rmd’

--- re-building ‘heatmaps.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
[WARNING] Citeproc: citation factorplot not found
--- finished re-building ‘heatmaps.Rmd’

--- re-building ‘sig_diffs_explanation.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘sig_diffs_explanation.Rmd’

--- re-building ‘significance_brackets.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘significance_brackets.Rmd’

Warning: elapsed-time limit of 1 hours reached for sub-process
--- re-building ‘viztest_intro_v2.Rmd’ using rmarkdown


Quitting from viztest_intro_v2.Rmd:235-240 [unnamed-chunk-11]
Execution halted
SUMMARY: processing the following file failed:
  ‘viztest_intro_v2.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [7s/29s] OK
* checking HTML version of manual ... [2s/21s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-noLD/VizTest.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:18:07, 1399.85 + 39.01