Rapid builds (Linux only) of a subset of BioC 3.21<BR>Report updated every 6 hours

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88118) -- "How About a Twenty-Six"	870
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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: 2.37.0

Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAbiolinks

StartedAt: 2025-04-15 13:32:20 -0400 (Tue, 15 Apr 2025)

EndedAt: 2025-04-15 13:35:39 -0400 (Tue, 15 Apr 2025)

EllapsedTime: 198.4 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 clinical.Rmd:67-77 [BCR_Biotab]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `GDCdownload.aux()`:
! 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.
---
Backtrace:
    ▆
 1. └─TCGAbiolinks::GDCdownload(query)
 2.   └─base::tryCatch(...) at TCGAbiolinks/R/download.R:159:17
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
 6.           └─TCGAbiolinks:::GDCdownload.by.chunk(...) at TCGAbiolinks/R/download.R:169:25
 7.             └─TCGAbiolinks:::GDCdownload.aux(...) at TCGAbiolinks/R/download.R:244:13
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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