Multiple platform build/check report for BioC 3.21 - BUILD results for GenomicDataCommons on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4827
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4608
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4549
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4581
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 GenomicDataCommons on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: GenomicDataCommons

Version: 1.32.1

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

StartedAt: 2025-09-23 01:44:29 -0000 (Tue, 23 Sep 2025)

EndedAt: 2025-09-23 01:46:48 -0000 (Tue, 23 Sep 2025)

EllapsedTime: 139.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicDataCommons
###
##############################################################################
##############################################################################


* checking for file ‘GenomicDataCommons/DESCRIPTION’ ... OK
* preparing ‘GenomicDataCommons’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘overview.Rmd’ using rmarkdown
--- finished re-building ‘overview.Rmd’

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

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

Quitting from somatic_mutations.Rmd:68-75 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [api.gdc.cancer.gov]: Connection timed out after 10002 milliseconds
---
Backtrace:
     ▆
  1. ├─tibble::as_tibble(...)
  2. ├─GenomicDataCommons::results_all(...)
  3. ├─GenomicDataCommons::filter(...)
  4. ├─GenomicDataCommons::ssms()
  5. │ └─GenomicDataCommons::query("ssms", ...)
  6. │   ├─base::structure(...)
  7. │   ├─GenomicDataCommons::default_fields(entity)
  8. │   └─GenomicDataCommons:::default_fields.character(entity)
  9. │     ├─base::subset(mapping(x), defaults)
 10. │     └─GenomicDataCommons::mapping(x)
 11. │       └─GenomicDataCommons:::.get_mapping_json(endpoint)
 12. │         └─GenomicDataCommons:::.gdc_get(sprintf("%s/%s", endpoint, "_mapping"))
 13. │           └─httr::GET(uri, add_headers(`X-Auth-Token` = token), ...)
 14. │             └─httr:::request_perform(req, hu$handle$handle)
 15. │               ├─httr:::request_fetch(req$output, req$url, handle)
 16. │               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 17. │                 └─curl::curl_fetch_memory(url, handle = handle)
 18. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'somatic_mutations.Rmd' failed with diagnostics:
Timeout was reached [api.gdc.cancer.gov]: Connection timed out after 10002 milliseconds
--- failed re-building ‘somatic_mutations.Rmd’

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

Error: Vignette re-building failed.
Execution halted