| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-13 12:06 -0400 (Sat, 13 Sep 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" | 4719 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4538 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4522 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4543 |
| 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 801/2327 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gemma.R 3.5.5 (landing page) Ogan Mancarci
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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: 3.5.5 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data gemma.R |
| StartedAt: 2025-09-12 00:46:07 -0000 (Fri, 12 Sep 2025) |
| EndedAt: 2025-09-12 01:05:24 -0000 (Fri, 12 Sep 2025) |
| EllapsedTime: 1156.4 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
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$result.ID %>% ...
2. ├─BiocGenerics::lapply(...)
3. ├─base::lapply(...)
4. │ └─FUN(X[[i]], ...)
5. │ └─gemma.R::get_differential_expression_values(resultSets = x)
6. │ └─base::lapply(...)
7. │ └─gemma.R (local) FUN(X[[i]], ...)
8. │ └─gemma.R:::.getResultSets(x, memoised = memoised)
9. │ └─gemma.R:::mem.getResultSets(...)
10. │ ├─gemma.R (local) mem_call(...)
11. │ │ ├─base::withVisible(eval(mc, parent.frame()))
12. │ │ └─base::eval(mc, parent.frame())
13. │ │ └─base::eval(mc, parent.frame())
14. │ └─gemma.R (local) `<fn>`(...)
15. │ ├─gemma.R:::.body(...)
16. │ │ └─base::eval(requestExpr, envir = envWhere)
17. │ │ └─base::eval(requestExpr, envir = envWhere)
18. │ └─httr::GET(...)
19. │ └─httr:::request_perform(req, hu$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