Build/check report for BioC 3.23 - BUILD results for GenomicDataCommons 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"	4823
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BUILD results for GenomicDataCommons on nebbiolo1

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

Version: 1.35.1

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

StartedAt: 2025-11-11 17:47:55 -0500 (Tue, 11 Nov 2025)

EndedAt: 2025-11-11 17:49:12 -0500 (Tue, 11 Nov 2025)

EllapsedTime: 76.1 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 GenomicDataCommons
###
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* checking for file ‘GenomicDataCommons/DESCRIPTION’ ... OK
* preparing ‘GenomicDataCommons’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘overview.Rmd’ using rmarkdown

Quitting from overview.Rmd:109-111 [statusQS]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
---
Backtrace:
    ▆
 1. ├─GenomicDataCommons::status()
 2. │ └─GenomicDataCommons:::.gdc_get(...)
 3. │   └─httr::GET(uri, add_headers(`X-Auth-Token` = token), ...)
 4. │     └─httr:::request_perform(req, hu$handle$handle)
 5. │       ├─httr:::request_fetch(req$output, req$url, handle)
 6. │       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 7. │         └─curl::curl_fetch_memory(url, handle = handle)
 8. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'overview.Rmd' failed with diagnostics:
Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
--- failed re-building ‘overview.Rmd’

--- re-building ‘questions-and-answers.Rmd’ using rmarkdown

Quitting from questions-and-answers.Rmd:31-38 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
---
Backtrace:
     ▆
  1. ├─GenomicDataCommons::filter(...)
  2. ├─GenomicDataCommons::files()
  3. │ └─GenomicDataCommons::query("files", ...)
  4. │   ├─base::structure(...)
  5. │   ├─GenomicDataCommons::default_fields(entity)
  6. │   └─GenomicDataCommons:::default_fields.character(entity)
  7. │     ├─base::subset(mapping(x), defaults)
  8. │     └─GenomicDataCommons::mapping(x)
  9. │       └─GenomicDataCommons:::.get_mapping_json(endpoint)
 10. │         └─GenomicDataCommons:::.gdc_get(sprintf("%s/%s", endpoint, "_mapping"))
 11. │           └─httr::GET(uri, add_headers(`X-Auth-Token` = token), ...)
 12. │             └─httr:::request_perform(req, hu$handle$handle)
 13. │               ├─httr:::request_fetch(req$output, req$url, handle)
 14. │               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 15. │                 └─curl::curl_fetch_memory(url, handle = handle)
 16. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'questions-and-answers.Rmd' failed with diagnostics:
Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
--- failed re-building ‘questions-and-answers.Rmd’

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

SUMMARY: processing the following files failed:
  ‘overview.Rmd’ ‘questions-and-answers.Rmd’

Error: Vignette re-building failed.
Execution halted