| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-13 12:07 -0400 (Mon, 13 Oct 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" | 4864 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
| 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 906/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GOstats 2.75.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the GOstats package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GOstats.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: GOstats |
| Version: 2.75.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data GOstats |
| StartedAt: 2025-10-10 01:07:28 -0000 (Fri, 10 Oct 2025) |
| EndedAt: 2025-10-10 01:18:22 -0000 (Fri, 10 Oct 2025) |
| EllapsedTime: 653.8 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 GOstats
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* checking for file ‘GOstats/DESCRIPTION’ ... OK
* preparing ‘GOstats’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GOstatsForUnsupportedOrganisms.Rmd’ using rmarkdown
Warning: call dbDisconnect() when finished working with a connection
Quitting from GOstatsForUnsupportedOrganisms.Rmd:126-131 [KEGGFrame object]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [rest.kegg.jp]:
Connection timed out after 10002 milliseconds
---
Backtrace:
▆
1. ├─AnnotationDbi::KEGGFrame(keggframeData, organism = "Homo sapiens")
2. ├─AnnotationDbi::KEGGFrame(keggframeData, organism = "Homo sapiens")
3. │ ├─base::data.frame(keggList("pathway"))
4. │ └─KEGGREST::keggList("pathway")
5. │ └─KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
6. │ └─httr::GET(url)
7. │ └─httr:::request_perform(req, hu$handle$handle)
8. │ ├─httr:::request_fetch(req$output, req$url, handle)
9. │ └─httr:::request_fetch.write_memory(req$output, req$url, handle)
10. │ └─curl::curl_fetch_memory(url, handle = handle)
11. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GOstatsForUnsupportedOrganisms.Rmd' failed with diagnostics:
Timeout was reached [rest.kegg.jp]:
Connection timed out after 10002 milliseconds
--- failed re-building ‘GOstatsForUnsupportedOrganisms.Rmd’
--- re-building ‘GOstatsHyperG.Rmd’ using rmarkdown
--- finished re-building ‘GOstatsHyperG.Rmd’
--- re-building ‘GOvis.Rmd’ using rmarkdown
Warning in doTryCatch(return(expr), name, parentenv, handler) :
"nodeAttrs" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
zero-length arrow is of indeterminate angle and so skipped