Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-04 11:47 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 802/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gemma.R 3.4.5 (landing page) Ogan Mancarci
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | 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: 3.4.5 |
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data gemma.R |
StartedAt: 2025-08-01 00:56:06 -0000 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 01:03:21 -0000 (Fri, 01 Aug 2025) |
EllapsedTime: 435.1 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### 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]: Connection timed out after 10001 milliseconds --- 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]: Connection timed out after 10001 milliseconds --- failed re-building ‘metanalysis.Rmd’ SUMMARY: processing the following file failed: ‘metanalysis.Rmd’ Error: Vignette re-building failed. Execution halted