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This page was generated on 2025-10-11 12:06 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4586
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

Package 805/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gemma.R 3.5.13  (landing page)
Ogan Mancarci
Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 Oct 2025)
git_url: https://git.bioconductor.org/packages/gemma.R
git_branch: devel
git_last_commit: b746483
git_last_commit_date: 2025-10-09 17:44:18 -0400 (Thu, 09 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


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: 3.5.11
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data gemma.R
StartedAt: 2025-10-10 00:42:31 -0000 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 01:00:13 -0000 (Fri, 10 Oct 2025)
EllapsedTime: 1062.3 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]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
---
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]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
--- failed re-building ‘metanalysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted