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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 185/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.39.0  (landing page)
Martin Morgan
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/BiocParallel
git_branch: devel
git_last_commit: aa329b3
git_last_commit_date: 2024-04-30 10:29:39 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.4 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for BiocParallel on palomino4

To the developers/maintainers of the BiocParallel package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocParallel.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BiocParallel
Version: 1.39.0
Command: chmod a+r BiocParallel -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data BiocParallel
StartedAt: 2024-06-09 17:31:35 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 17:35:22 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 227.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r BiocParallel -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data BiocParallel
###
##############################################################################
##############################################################################


* checking for file 'BiocParallel/DESCRIPTION' ... OK
* preparing 'BiocParallel':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'Introduction_To_BiocParallel.Rmd' using rmarkdown
--- finished re-building 'Introduction_To_BiocParallel.Rmd'

--- re-building 'Random_Numbers.Rmd' using rmarkdown
--- finished re-building 'Random_Numbers.Rmd'

--- re-building 'BiocParallel_BatchtoolsParam.Rnw' using knitr
texify: major issue: User/administrator updates are out-of-sync.
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "BiocParallel_BatchtoolsParam.tex" --max-iterations=20 -I "F:/biocbuild/bbs-3.20-bioc/R/share/texmf/tex/latex" -I "F:/biocbuild/bbs-3.20-bioc/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'BiocParallel_BatchtoolsParam.Rnw' failed with diagnostics:
running 'texi2dvi' on 'BiocParallel_BatchtoolsParam.tex' failed

LaTeX errors:
gnettes/BiocParallel_BatchtoolsParam.tex:78: Package xcolor Error: Undefined co
lor `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/BiocParallel_BatchtoolsParam.tex:160: Package xcolor Error: Undefined c
olor `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/BiocParallel_BatchtoolsParam.tex:232: Package xcolor Error: Undefined c
olor `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/BiocParallel_BatchtoolsParam.tex:336: Package xcolor Error: Undefined c
olor `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/BiocParallel_BatchtoolsParam.tex:362: Package xcolor Error: Undefined c
olor `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.

--- failed re-building 'BiocParallel_BatchtoolsParam.Rnw'

--- re-building 'Errors_Logs_And_Debugging.Rnw' using knitr
texify: major issue: User/administrator updates are out-of-sync.
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "Errors_Logs_And_Debugging.tex" --max-iterations=20 -I "F:/biocbuild/bbs-3.20-bioc/R/share/texmf/tex/latex" -I "F:/biocbuild/bbs-3.20-bioc/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'Errors_Logs_And_Debugging.Rnw' failed with diagnostics:
running 'texi2dvi' on 'Errors_Logs_And_Debugging.tex' failed

LaTeX errors:
gnettes/Errors_Logs_And_Debugging.tex:79: Package xcolor Error: Undefined color
 `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:91: Package xcolor Error: Undefined color
 `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:110: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:123: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:150: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:173: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:201: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:216: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:264: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:316: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:355: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:369: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:415: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:426: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:441: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:473: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:501: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:513: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:558: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:580: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:612: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:632: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:654: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:676: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:752: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:774: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:826: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:925: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:944: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:952: Package xcolor Error: Undefined colo
r `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:1037: Package xcolor Error: Undefined col
or `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
gnettes/Errors_Logs_And_Debugging.tex:1063: Package xcolor Error: Undefined col
or `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.

--- failed re-building 'Errors_Logs_And_Debugging.Rnw'

SUMMARY: processing the following files failed:
  'BiocParallel_BatchtoolsParam.Rnw' 'Errors_Logs_And_Debugging.Rnw'

Error: Vignette re-building failed.
Execution halted