Multiple platform build/check report for BioC 3.23 - BUILD results for gemma.R on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 alpha (2026-04-05 r89794)	4961
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 alpha (2026-04-08 r89818)	4690
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4627
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 gemma.R on kunpeng2

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

Version: 3.7.1

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

StartedAt: 2026-04-16 23:41:52 -0000 (Thu, 16 Apr 2026)

EndedAt: 2026-04-17 00:02:33 -0000 (Fri, 17 Apr 2026)

EllapsedTime: 1241.4 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 gemma.R
###
##############################################################################
##############################################################################


* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* preparing ‘gemma.R’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gemma.R.Rmd’ using rmarkdown
Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘gemma.R.Rmd’

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

Quitting from metadata.Rmd:287-291 [unnamed-chunk-17]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [gemma.msl.ubc.ca]: Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
---
Backtrace:
     ▆
  1. ├─gemma.R::get_differential_expression_values("GSE48962")
  2. │ └─base::lapply(...)
  3. │   └─gemma.R (local) FUN(X[[i]], ...)
  4. │     └─gemma.R:::.getResultSets(x, memoised = memoised)
  5. │       └─gemma.R:::mem.getResultSets(...)
  6. │         ├─gemma.R (local) mem_call(...)
  7. │         │ ├─base::withVisible(eval(mc, parent.frame()))
  8. │         │ └─base::eval(mc, parent.frame())
  9. │         │   └─base::eval(mc, parent.frame())
 10. │         └─gemma.R (local) `<fn>`(...)
 11. │           └─gemma.R:::.body(...)
 12. │             ├─base::eval(requestExpr)
 13. │             │ └─base::eval(requestExpr)
 14. │             └─httr::GET(...)
 15. │               └─httr:::request_perform(req, hu$handle$handle)
 16. │                 ├─httr:::request_fetch(req$output, req$url, handle)
 17. │                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 18. │                   └─curl::curl_fetch_memory(url, handle = handle)
 19. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metadata.Rmd' failed with diagnostics:
Timeout was reached [gemma.msl.ubc.ca]: Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
--- failed re-building ‘metadata.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted