Build/check report for BioC 3.23 - BUILD results for TCGAbiolinks on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4821
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BUILD results for TCGAbiolinks on nebbiolo1

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

Version: 2.39.0

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

StartedAt: 2025-11-07 20:24:09 -0500 (Fri, 07 Nov 2025)

EndedAt: 2025-11-07 20:30:40 -0500 (Fri, 07 Nov 2025)

EllapsedTime: 390.8 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/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 (it is needed 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
--- finished 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

Quitting from query.Rmd:141-154 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection to 'https://api.gdc.cancer.gov/projects/TCGA-LGG?expand=summary,summary.data_categories&pretty=true'
---
Backtrace:
     ▆
  1. └─TCGAbiolinks::GDCquery(...)
  2.   └─TCGAbiolinks:::getGDCquery(...) at TCGAbiolinks/R/query.R:223:9
  3.     ├─base::paste0("size=", getNbFiles(project, data.category)) at TCGAbiolinks/R/query.R:621:5
  4.     └─TCGAbiolinks:::getNbFiles(project, data.category) at TCGAbiolinks/R/query.R:621:5
  5.       └─TCGAbiolinks::getProjectSummary(project) at TCGAbiolinks/R/api.R:329:9
  6.         └─jsonlite::fromJSON(url, simplifyDataFrame = TRUE) at TCGAbiolinks/R/api.R:291:5
  7.           └─jsonlite:::parse_and_simplify(...)
  8.             └─jsonlite:::parseJSON(txt, bigint_as_char)
  9.               └─jsonlite:::parse_con(txt, bigint_as_char)
 10.                 ├─base::open(con, "rb")
 11.                 └─base::open.connection(con, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'query.Rmd' failed with diagnostics:
cannot open the connection to 'https://api.gdc.cancer.gov/projects/TCGA-LGG?expand=summary,summary.data_categories&pretty=true'
--- failed 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:
  ‘query.Rmd’

Error: Vignette re-building failed.
Execution halted