Build/check report for BioC 3.23 - BUILD results for gemma.R 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
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 nebbiolo1

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.

raw results

Summary

Package: gemma.R

Version: 3.7.0

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

StartedAt: 2025-11-11 17:45:07 -0500 (Tue, 11 Nov 2025)

EndedAt: 2025-11-11 17:49:06 -0500 (Tue, 11 Nov 2025)

EllapsedTime: 238.2 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 gemma.R
###
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* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* preparing ‘gemma.R’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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:468-484 [unnamed-chunk-20]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [gemma.msl.ubc.ca]:
SSL connection timeout
---
Backtrace:
     ▆
  1. ├─gemma.R::get_dataset_object(...)
  2. │ └─unique_sets %>% ...
  3. ├─base::lapply(...)
  4. │ └─gemma.R (local) FUN(X[[i]], ...)
  5. │   └─gemma.R::get_dataset_samples(dataset, memoised = memoised)
  6. │     └─gemma.R:::memget_dataset_samples(...)
  7. │       ├─gemma.R (local) mem_call(...)
  8. │       │ ├─base::withVisible(eval(mc, parent.frame()))
  9. │       │ └─base::eval(mc, parent.frame())
 10. │       │   └─base::eval(mc, parent.frame())
 11. │       └─gemma.R (local) `<fn>`(...)
 12. │         └─gemma.R:::.body(...)
 13. │           ├─base::eval(requestExpr)
 14. │           │ └─base::eval(requestExpr)
 15. │           └─httr::GET(...)
 16. │             └─httr:::request_perform(req, hu$handle$handle)
 17. │               ├─httr:::request_fetch(req$output, req$url, handle)
 18. │               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 19. │                 └─curl::curl_fetch_memory(url, handle = handle)
 20. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metanalysis.Rmd' failed with diagnostics:
Timeout was reached [gemma.msl.ubc.ca]:
SSL connection timeout
--- failed re-building ‘metanalysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted