Multiple platform build/check report for BioC 3.23 - BUILD results for CBN2Path on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4808
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4542
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*

BUILD results for CBN2Path on nebbiolo1

To the developers/maintainers of the CBN2Path package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CBN2Path.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: CBN2Path

Version: 1.1.4

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data CBN2Path

StartedAt: 2026-01-21 16:41:47 -0500 (Wed, 21 Jan 2026)

EndedAt: 2026-01-21 16:54:41 -0500 (Wed, 21 Jan 2026)

EllapsedTime: 773.6 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data CBN2Path
###
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* checking for file ‘CBN2Path/DESCRIPTION’ ... OK
* preparing ‘CBN2Path’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘CBN2Path.Rmd’ using rmarkdown

Quitting from CBN2Path.Rmd:54-63 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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. └─CBN2Path::getRawTCGAData("TCGA-BLCA")
 2.   └─TCGAbiolinks::GDCdownload(query)
 3.     └─base::tryCatch(...)
 4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.           └─value[[3L]](cond)
 7.             └─TCGAbiolinks:::GDCdownload.by.chunk(...)
 8.               └─TCGAbiolinks:::GDCdownload.aux(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'CBN2Path.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 ‘CBN2Path.Rmd’

SUMMARY: processing the following file failed:
  ‘CBN2Path.Rmd’

Error: Vignette re-building failed.
Execution halted