Paul Pavlidis
| Snapshot Date: 2026-05-05 13:45 -0400 (Tue, 05 May 2026) |
| git_url: https://git.bioconductor.org/packages/gemma.R |
| git_branch: devel |
| git_last_commit: e02b4b7 |
| git_last_commit_date: 2026-04-28 08:59:04 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-06 11:34 -0400 (Wed, 06 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4878 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4663 |
| 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 814/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gemma.R 3.9.0 (landing page) Paul Pavlidis
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
| See other builds for gemma.R in R Universe. | ||||||||||||||
|
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. |
| Package: gemma.R |
| Version: 3.9.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data gemma.R |
| StartedAt: 2026-05-05 03:12:26 -0000 (Tue, 05 May 2026) |
| EndedAt: 2026-05-05 03:29:04 -0000 (Tue, 05 May 2026) |
| EllapsedTime: 997.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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### Running command:
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### /home/biocbuild/R/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 to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gemma.R.Rmd’ using rmarkdown
Quitting from gemma.R.Rmd:158-164 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'x' in selecting a method for function 'head': SSL connect error [gemma.msl.ubc.ca]:
Recv failure: Connection reset by peer
---
Backtrace:
▆
1. ├─... %>% gemma_kable
2. ├─gemma.R::gemma_kable(.)
3. │ └─base::ncol(table)
4. ├─utils::head(.)
5. ├─dplyr::select(...)
6. ├─gemma.R::get_all_pages(.)
7. │ ├─... %>% do.call(binder, .)
8. │ └─base::lapply(...)
9. │ └─gemma.R (local) FUN(X[[i]], ...)
10. │ ├─base::do.call(attr$env$fname, step_args)
11. │ └─gemma.R::get_datasets(...)
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. ├─base::do.call(binder, .)
21. ├─curl:::raise_libcurl_error(...)
22. │ └─base::stop(e)
23. └─base (local) `<fn>`(`<crl_r___>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'gemma.R.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'head': SSL connect error [gemma.msl.ubc.ca]:
Recv failure: Connection reset by peer
--- failed re-building ‘gemma.R.Rmd’
--- re-building ‘metadata.Rmd’ using rmarkdown
Quitting from metadata.Rmd:90-96 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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_dataset_samples("GSE48962")
2. │ └─gemma.R:::memget_dataset_samples(...)
3. │ ├─gemma.R (local) mem_call(...)
4. │ │ ├─base::withVisible(eval(mc, parent.frame()))
5. │ │ └─base::eval(mc, parent.frame())
6. │ │ └─base::eval(mc, parent.frame())
7. │ └─gemma.R (local) `<fn>`(...)
8. │ └─gemma.R:::.body(...)
9. │ ├─base::eval(requestExpr)
10. │ │ └─base::eval(requestExpr)
11. │ └─httr::GET(...)
12. │ └─httr:::request_perform(req, hu$handle$handle)
13. │ ├─httr:::request_fetch(req$output, req$url, handle)
14. │ └─httr:::request_fetch.write_memory(req$output, req$url, handle)
15. │ └─curl::curl_fetch_memory(url, handle = handle)
16. └─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
Quitting from metanalysis.Rmd:64-67 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [gemma.msl.ubc.ca]:
Connection timed out after 10001 milliseconds
---
Backtrace:
▆
1. ├─gemma.R::search_annotations("parkinson's")
2. │ └─gemma.R:::memsearch_annotations(...)
3. │ ├─gemma.R (local) mem_call(...)
4. │ │ ├─base::withVisible(eval(mc, parent.frame()))
5. │ │ └─base::eval(mc, parent.frame())
6. │ │ └─base::eval(mc, parent.frame())
7. │ └─gemma.R (local) `<fn>`(...)
8. │ └─gemma.R:::.body(...)
9. │ ├─base::eval(requestExpr)
10. │ │ └─base::eval(requestExpr)
11. │ └─httr::GET(...)
12. │ └─httr:::request_perform(req, hu$handle$handle)
13. │ ├─httr:::request_fetch(req$output, req$url, handle)
14. │ └─httr:::request_fetch.write_memory(req$output, req$url, handle)
15. │ └─curl::curl_fetch_memory(url, handle = handle)
16. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'metanalysis.Rmd' failed with diagnostics:
Timeout was reached [gemma.msl.ubc.ca]:
Connection timed out after 10001 milliseconds
--- failed re-building ‘metanalysis.Rmd’
SUMMARY: processing the following files failed:
‘gemma.R.Rmd’ ‘metadata.Rmd’ ‘metanalysis.Rmd’
Error: Vignette re-building failed.
Execution halted