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This page was generated on 2026-01-07 11:34 -0500 (Wed, 07 Jan 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" 4815
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4593
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 1248/2332HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methodical 1.7.0  (landing page)
Richard Heery
Snapshot Date: 2026-01-06 13:40 -0500 (Tue, 06 Jan 2026)
git_url: https://git.bioconductor.org/packages/methodical
git_branch: devel
git_last_commit: e40174f
git_last_commit_date: 2026-01-04 15:48:58 -0500 (Sun, 04 Jan 2026)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for methodical on nebbiolo1

To the developers/maintainers of the methodical package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methodical.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: methodical
Version: 1.7.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data methodical
StartedAt: 2026-01-06 18:32:51 -0500 (Tue, 06 Jan 2026)
EndedAt: 2026-01-06 18:46:32 -0500 (Tue, 06 Jan 2026)
EllapsedTime: 821.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data methodical
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* checking for file ‘methodical/DESCRIPTION’ ... OK
* preparing ‘methodical’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘calculating_methylation_transcription_correlations.Rmd’ using rmarkdown
--- finished re-building ‘calculating_methylation_transcription_correlations.Rmd’

--- re-building ‘working_with_meth_rses.Rmd’ using rmarkdown

Quitting from working_with_meth_rses.Rmd:221-245 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `methodical::extractMethSitesFromGenome()`:
! unused argument (search_both_strands = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'working_with_meth_rses.Rmd' failed with diagnostics:
unused argument (search_both_strands = FALSE)
--- failed re-building ‘working_with_meth_rses.Rmd’

SUMMARY: processing the following file failed:
  ‘working_with_meth_rses.Rmd’

Error: Vignette re-building failed.
Execution halted