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This page was generated on 2025-04-22 13:14 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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 222/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biostrings 2.76.0  (landing page)
Hervé Pagès
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/Biostrings
git_branch: RELEASE_3_21
git_last_commit: 2e04124
git_last_commit_date: 2025-04-15 09:17:28 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  YES
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  

BUILD results for Biostrings on palomino7

To the developers/maintainers of the Biostrings package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Biostrings.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: Biostrings
Version: 2.76.0
Command: chmod a+r Biostrings -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data Biostrings
StartedAt: 2025-04-21 17:46:10 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 17:48:41 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 150.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r Biostrings -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data Biostrings
###
##############################################################################
##############################################################################


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

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

--- re-building 'Biostrings2Classes.Rnw' using Sweave
Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 1033
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "Biostrings2Classes.tex" ' had status 1033
Error: processing vignette 'Biostrings2Classes.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'Biostrings2Classes.pdf' for vignette with name 'Biostrings2Classes' and engine 'utils::Sweave'. The following files exist in working directory 'E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmpw36QNF\Rbuild4b905e7e7440\Biostrings\vignettes': 'Biostrings2Classes.Rnw' (8514 bytes), 'Biostrings2Classes.tex' (12527 bytes), 'BiostringsQuickOverview.Rnw' (9332 bytes), 'MultipleAlignments.R' (4544 bytes), 'MultipleAlignments.Rmd' (9923 bytes), 'MultipleAlignments.html' (670322 bytes), 'PairwiseAlignments.Rnw' (1206 bytes), 'SolexaYi2-benchmark.txt' (16707 bytes), 'badTree.png' (4498 bytes), 'goodTree.png' (4665 bytes), 'matchprobes.R' (3391 bytes), 'matchprobes.Rmd' (7906 bytes), 'matchprobes.html' (795419 bytes)
--- failed re-building 'Biostrings2Classes.Rnw'

--- re-building 'BiostringsQuickOverview.Rnw' using Sweave
Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 1033
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "BiostringsQuickOverview.tex" ' had status 1033
Error: processing vignette 'BiostringsQuickOverview.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'BiostringsQuickOverview.pdf' for vignette with name 'BiostringsQuickOverview' and engine 'utils::Sweave'. The following files exist in working directory 'E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmpw36QNF\Rbuild4b905e7e7440\Biostrings\vignettes': 'Biostrings2Classes.R' (3765 bytes), 'Biostrings2Classes.Rnw' (8514 bytes), 'Biostrings2Classes.tex' (12527 bytes), 'BiostringsQuickOverview.Rnw' (9332 bytes), 'BiostringsQuickOverview.tex' (9634 bytes), 'MultipleAlignments.R' (4544 bytes), 'MultipleAlignments.Rmd' (9923 bytes), 'MultipleAlignments.html' (670322 bytes), 'PairwiseAlignments.Rnw' (1206 bytes), 'SolexaYi2-benchmark.txt' (16707 bytes), 'badTree.png' (4498 bytes), 'goodTree.png' (4665 bytes), 'matchprobes.R' (3391 bytes), 'matchprobes.Rmd' (7906 bytes), 'matchprobes.html' (795419 bytes)
--- failed re-building 'BiostringsQuickOverview.Rnw'

--- re-building 'PairwiseAlignments.Rnw' using Sweave
Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 1033
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "PairwiseAlignments.tex" ' had status 1033
Error: processing vignette 'PairwiseAlignments.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'PairwiseAlignments.pdf' for vignette with name 'PairwiseAlignments' and engine 'utils::Sweave'. The following files exist in working directory 'E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmpw36QNF\Rbuild4b905e7e7440\Biostrings\vignettes': 'Biostrings2Classes.R' (3765 bytes), 'Biostrings2Classes.Rnw' (8514 bytes), 'Biostrings2Classes.tex' (12527 bytes), 'BiostringsQuickOverview.R' (65 bytes), 'BiostringsQuickOverview.Rnw' (9332 bytes), 'BiostringsQuickOverview.tex' (9634 bytes), 'MultipleAlignments.R' (4544 bytes), 'MultipleAlignments.Rmd' (9923 bytes), 'MultipleAlignments.html' (670322 bytes), 'PairwiseAlignments.Rnw' (1206 bytes), 'PairwiseAlignments.tex' (1278 bytes), 'SolexaYi2-benchmark.txt' (16707 bytes), 'badTree.png' (4498 bytes), 'goodTree.png' (4665 bytes), 'matchprobes.R' (3391 bytes), 'matchprobes.Rmd' (7906 bytes), 'matchprobes.html' (795419 bytes)
--- failed re-building 'PairwiseAlignments.Rnw'

SUMMARY: processing the following files failed:
  'Biostrings2Classes.Rnw' 'BiostringsQuickOverview.Rnw'
  'PairwiseAlignments.Rnw'

Error: Vignette re-building failed.
Execution halted