Back to Workflows build report for BioC 3.22

This page was generated on 2025-10-21 16:30 -0400 (Tue, 21 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4888
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
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 28/29HostnameOS / ArchINSTALLBUILD
TCGAWorkflow 1.33.0  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2025-10-21 12:45 -0400 (Tue, 21 Oct 2025)
git_url: https://git.bioconductor.org/packages/TCGAWorkflow
git_branch: devel
git_last_commit: 9635550
git_last_commit_date: 2025-04-15 10:29:17 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR    ERROR  
lconwaymacOS 12.7.6 Monterey / x86_64  OK    ERROR  

BUILD results for TCGAWorkflow on lconway

To the developers/maintainers of the TCGAWorkflow package:
- 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: TCGAWorkflow
Version: 1.33.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAWorkflow
StartedAt: 2025-10-21 13:11:08 -0400 (Tue, 21 Oct 2025)
EndedAt: 2025-10-21 13:17:30 -0400 (Tue, 21 Oct 2025)
EllapsedTime: 382.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAWorkflow
###
##############################################################################
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* checking for file ‘TCGAWorkflow/DESCRIPTION’ ... OK
* preparing ‘TCGAWorkflow’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘TCGAWorkflow.Rmd’ using rmarkdown
2025-10-21 13:14:27.226 R[49270:598132118] XType: com.apple.fonts is not accessible.
2025-10-21 13:14:27.227 R[49270:598132118] XType: XTFontStaticRegistry is enabled.

Quitting from TCGAWorkflow.Rmd:1691-1713 [getTagMatrix]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `keepStandardChromosomes()`:
! could not find function "keepStandardChromosomes"
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'TCGAWorkflow.Rmd' failed with diagnostics:
could not find function "keepStandardChromosomes"
--- failed re-building ‘TCGAWorkflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted