Back to Workflows build report for BioC 3.22

This page was generated on 2025-08-15 16:30 -0400 (Fri, 15 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4554
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
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: 2025-08-15 12:45 -0400 (Fri, 15 Aug 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  
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  

BUILD results for TCGAWorkflow on palomino8

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: chmod a+r TCGAWorkflow -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data TCGAWorkflow
StartedAt: 2025-08-15 13:18:54 -0400 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 13:46:14 -0400 (Fri, 15 Aug 2025)
EllapsedTime: 1640.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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###
### Running command:
###
###   chmod a+r TCGAWorkflow -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe 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

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