| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-11-12 11:57 -0500 (Wed, 12 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| 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 | ||||
| Package 812/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gemma.R 3.6.0 (landing page) Ogan Mancarci
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. |
| Package: gemma.R |
| Version: 3.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 gemma.R |
| StartedAt: 2025-11-11 17:49:29 -0500 (Tue, 11 Nov 2025) |
| EndedAt: 2025-11-11 17:52:24 -0500 (Tue, 11 Nov 2025) |
| EllapsedTime: 175.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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:88-109 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'x' in selecting a method for function 'head': Timeout was reached [gemma.msl.ubc.ca]:
SSL connection timeout
---
Backtrace:
▆
1. ├─... %>% gemma_kable
2. ├─gemma.R::gemma_kable(.)
3. │ └─base::ncol(table)
4. ├─utils::head(.)
5. ├─dplyr::select(...)
6. ├─gemma.R::get_datasets(taxa = c("mouse", "human"))
7. │ └─gemma.R:::memget_datasets(...)
8. │ ├─gemma.R (local) mem_call(...)
9. │ │ ├─base::withVisible(eval(mc, parent.frame()))
10. │ │ └─base::eval(mc, parent.frame())
11. │ │ └─base::eval(mc, parent.frame())
12. │ └─gemma.R (local) `<fn>`(...)
13. │ └─gemma.R:::.body(...)
14. │ ├─base::eval(requestExpr)
15. │ │ └─base::eval(requestExpr)
16. │ └─httr::GET(...)
17. │ └─httr:::request_perform(req, hu$handle$handle)
18. │ ├─httr:::request_fetch(req$output, req$url, handle)
19. │ └─httr:::request_fetch.write_memory(req$output, req$url, handle)
20. │ └─curl::curl_fetch_memory(url, handle = handle)
21. ├─curl:::raise_libcurl_error(...)
22. │ └─base::stop(e)
23. └─base (local) `<fn>`(`<crl_rr__>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'gemma.R.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'head': Timeout was reached [gemma.msl.ubc.ca]:
SSL connection timeout
--- failed 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 files failed:
‘gemma.R.Rmd’ ‘metanalysis.Rmd’
Error: Vignette re-building failed.
Execution halted