* using log directory ‘/data/gannet/ripley/R/packages/tests-ATLAS/rapbase.Rcheck’
* using R Under development (unstable) (2023-06-19 r84569)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.1.0
    GNU Fortran (GCC) 13.1.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘rapbase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rapbase’ version ‘1.24.2’
* 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 ‘rapbase’ can be installed ... 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 R 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [62s/63s]
 [62s/63s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rapbase)
  > 
  > test_check("rapbase")
  /usr/bin/pandoc +RTS -K512m -RTS howWeDealWithPersonalData.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/2162994722369c.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file21629953e6ca7b --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/21629928a5a05.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file2162994eb174f0 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str2162997db61930.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/2162995d396961.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file21629930df9c18 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str2162991a0dc835.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/2162997b863ff0.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file2162995eb08619 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str216299417e59b2.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/2162995e10a9c4.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file2162992e294b26 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str216299a8e92f.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/21629946295856.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file2162992da8f6d3 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str2162991db1b16d.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/216299517326ae.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file2162996c080482 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str2162998a227d6.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/21629968c6d5aa.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file21629940fa59fa --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str2162991bd9951a.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/2162991e65d874.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file2162991f4618fd --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str216299772d6c15.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/216299754a0fff.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file2162997c2c132b --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str2162997020afa3.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/21629946d31546.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file21629955863134 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str2162994d41894b.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/2162997c778e36.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file2162996c1701c --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str2162995cf3166d.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/2162992009959f.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file2162991efbec92 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str216299523863a0.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/2162995e72fc9e.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file21629975612a16 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str216299380c3858.html 
       [,1]
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/21629923a145cb.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file2162998b97b54 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str216299485d505a.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/216299286ed5cb.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file2162993c159447 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str2162994800d67b.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/2162994e64bce.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file2162996d23ef33 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str2162997a5e8ffa.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/216299509f2f68.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file2162996ea202d7 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str2162991b3f10cb.html 
  /usr/bin/pandoc +RTS -K512m -RTS autoReportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/21629940b84d9d.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file2162991142fd7 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str2162993c6be7f6.html 
  /usr/bin/pandoc +RTS -K512m -RTS exportGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/21629947dc6ad8.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file2162993af0c52c --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight 
  /usr/bin/pandoc +RTS -K512m -RTS howWeDealWithPersonalData.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/21629914f6c46c.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file21629963f5af15 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight 
  /usr/bin/pandoc +RTS -K512m -RTS howWeDealWithPersonalData.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/2162997423b580.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file21629932bb99e8 --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight 
  /usr/bin/pandoc +RTS -K512m -RTS statsGuide.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/216299143b323a.html --lua-filter /data/gannet/ripley/R/test-dev/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-dev/rmarkdown/rmarkdown/lua/latex-div.lua --metadata-file /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/file21629920a9501a --self-contained --wrap preserve --mathjax --section-divs --template /data/gannet/ripley/R/test-dev/rmarkdown/rmd/fragment/default.html --no-highlight --include-in-header /tmp/RtmpoPfUl2/working_dir/Rtmp4Eb6KJ/rmarkdown-str21629945c3b58b.html 
  [ FAIL 1 | WARN 0 | SKIP 37 | PASS 247 ]
  
  ══ Skipped tests (37) ══════════════════════════════════════════════════════════
  • Possible lack of database infrastructure (35): 'test-auto-report-db.R:48:3',
    'test-auto-report-db.R:102:3', 'test-auto-report-db.R:107:3',
    'test-auto-report-db.R:112:3', 'test-auto-report-db.R:117:3',
    'test-dbConnection.R:35:3', 'test-dbConnection.R:96:3',
    'test-dbConnection.R:107:3', 'test-dbConnection.R:113:3',
    'test-dbConnection.R:122:3', 'test-dbConnection.R:130:3',
    'test-dbConnection.R:138:3', 'test-log.R:142:3', 'test-log.R:163:3',
    'test-log.R:168:3', 'test-log.R:184:3', 'test-log.R:189:3',
    'test-log.R:198:3', 'test-log.R:205:3', 'test-moduleExport.R:40:3',
    'test-moduleExport.R:99:3', 'test-moduleExport.R:115:5',
    'test-moduleExport.R:130:5', 'test-stagingData.R:130:3',
    'test-stagingData.R:170:3', 'test-stagingData.R:176:3',
    'test-stagingData.R:185:3', 'test-stagingData.R:193:3',
    'test-stagingData.R:199:3', 'test-stagingData.R:206:3',
    'test-stagingData.R:211:3', 'test-stagingData.R:216:3',
    'test-stagingData.R:221:3', 'test-stagingData.R:226:3',
    'test-stagingData.R:232:3'
  • Test skipped Windblows. Please fix later! (1): 'test-renderRmd.R:15:3'
  • cran autocheck false positive on debian (1):
    'test-auto-report-functions.R:220:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-auto-report-functions.R:213:3'): a report sceduled for today with startDate in future is not run ──
  `runAutoReport(dryRun = TRUE)` produced messages.
  
  [ FAIL 1 | WARN 0 | SKIP 37 | PASS 247 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* 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: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-ATLAS/rapbase.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:47.48, 96.30 + 10.15