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This page was generated on 2025-03-12 15:25 -0400 (Wed, 12 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 869
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Package 203/217HostnameOS / ArchINSTALLBUILDCHECK
TCGAbiolinks 2.35.3  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2025-03-12 12:00 -0400 (Wed, 12 Mar 2025)
git_url: https://git.bioconductor.org/packages/TCGAbiolinks
git_branch: devel
git_last_commit: 40752356
git_last_commit_date: 2025-02-17 17:42:36 -0400 (Mon, 17 Feb 2025)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped

BUILD results for TCGAbiolinks on teran2

To the developers/maintainers of the TCGAbiolinks 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: TCGAbiolinks
Version: 2.35.3
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAbiolinks
StartedAt: 2025-03-12 13:27:59 -0400 (Wed, 12 Mar 2025)
EndedAt: 2025-03-12 13:31:01 -0400 (Wed, 12 Mar 2025)
EllapsedTime: 182.5 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAbiolinks
###
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* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* preparing ‘TCGAbiolinks’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘analysis.Rmd’ using rmarkdown
--- finished re-building ‘analysis.Rmd’

--- re-building ‘casestudy.Rmd’ using rmarkdown
--- finished re-building ‘casestudy.Rmd’

--- re-building ‘classifiers.Rmd’ using rmarkdown
--- finished re-building ‘classifiers.Rmd’

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

Quitting from lines 68-77 [BCR_Biotab] (clinical.Rmd)
Error: processing vignette 'clinical.Rmd' failed with diagnostics:
There was an error in the download process (we might had a connection problem with GDC server).
Please run this function it again.
Try using method = `client` or setting files.per.chunk to a small number.
--- failed re-building ‘clinical.Rmd’

--- re-building ‘download_prepare.Rmd’ using rmarkdown
--- finished re-building ‘download_prepare.Rmd’

--- re-building ‘extension.Rmd’ using rmarkdown
--- finished re-building ‘extension.Rmd’

--- re-building ‘index.Rmd’ using rmarkdown
--- finished re-building ‘index.Rmd’

--- re-building ‘mutation.Rmd’ using rmarkdown
--- finished re-building ‘mutation.Rmd’

--- re-building ‘query.Rmd’ using rmarkdown
--- finished re-building ‘query.Rmd’

--- re-building ‘stemness_score.Rmd’ using rmarkdown
--- finished re-building ‘stemness_score.Rmd’

--- re-building ‘subtypes.Rmd’ using rmarkdown
--- finished re-building ‘subtypes.Rmd’

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

Error: Vignette re-building failed.
Execution halted