Multiple platform build/check report for BioC 3.22 - BUILD results for gemma.R on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4876
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"	4656
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4602
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4668
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 taishan

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: 3.6.0

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

StartedAt: 2025-11-25 01:50:43 -0000 (Tue, 25 Nov 2025)

EndedAt: 2025-11-25 02:01:21 -0000 (Tue, 25 Nov 2025)

EllapsedTime: 637.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### 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
--- finished re-building ‘metadata.Rmd’

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

Quitting from metanalysis.Rmd:225-238 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [gemma.msl.ubc.ca]:
Connection timed out after 10000 milliseconds
---
Backtrace:
     ▆
  1. ├─parkin_contrasts$result.ID %>% ...
  2. ├─BiocGenerics::lapply(...)
  3. ├─base::lapply(...)
  4. │ └─FUN(X[[i]], ...)
  5. │   └─gemma.R::get_differential_expression_values(resultSets = x)
  6. │     └─base::lapply(...)
  7. │       └─gemma.R (local) FUN(X[[i]], ...)
  8. │         └─gemma.R:::.getResultSets(x, memoised = memoised)
  9. │           └─gemma.R:::mem.getResultSets(...)
 10. │             ├─gemma.R (local) mem_call(...)
 11. │             │ ├─base::withVisible(eval(mc, parent.frame()))
 12. │             │ └─base::eval(mc, parent.frame())
 13. │             │   └─base::eval(mc, parent.frame())
 14. │             └─gemma.R (local) `<fn>`(...)
 15. │               └─gemma.R:::.body(...)
 16. │                 ├─base::eval(requestExpr)
 17. │                 │ └─base::eval(requestExpr)
 18. │                 └─httr::GET(...)
 19. │                   └─httr:::request_perform(req, hu$handle$handle)
 20. │                     ├─httr:::request_fetch(req$output, req$url, handle)
 21. │                     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 22. │                       └─curl::curl_fetch_memory(url, handle = handle)
 23. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metanalysis.Rmd' failed with diagnostics:
Timeout was reached [gemma.msl.ubc.ca]:
Connection timed out after 10000 milliseconds
--- failed re-building ‘metanalysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted