Sergio Picart-Armada
| Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/FELLA |
| git_branch: devel |
| git_last_commit: 8ef094f |
| git_last_commit_date: 2025-04-15 11:19:30 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-11 12:06 -0400 (Sat, 11 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 723/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FELLA 1.29.0 (landing page) Sergio Picart-Armada
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the FELLA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FELLA.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: FELLA |
| Version: 1.29.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data FELLA |
| StartedAt: 2025-10-10 00:32:49 -0000 (Fri, 10 Oct 2025) |
| EndedAt: 2025-10-10 01:00:26 -0000 (Fri, 10 Oct 2025) |
| EllapsedTime: 1657.6 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 FELLA
###
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* checking for file ‘FELLA/DESCRIPTION’ ... OK
* preparing ‘FELLA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘musmusculus.Rmd’ using rmarkdown
Warning: LaTeX Warning: You have requested package `/home/biocbuild/R/R-4.5.0/site-libra
Warning: ry/BiocStyle/resources/tex/Bioconductor',
Warning: but the package provides `Bioconductor'.
--- finished re-building ‘musmusculus.Rmd’
--- re-building ‘quickstart.Rmd’ using rmarkdown
--- finished re-building ‘quickstart.Rmd’
--- re-building ‘zebrafish.Rmd’ using rmarkdown
Quitting from zebrafish.Rmd:50-74 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [rest.kegg.jp]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
---
Backtrace:
x
1. +-FELLA::buildGraphFromKEGGREST(organism = "dre", filter.path = c("01100"))
2. | \-plyr::llply(...)
3. | +-plyr:::loop_apply(n, do.ply)
4. | \-plyr (local) `<fn>`(3L)
5. | \-FELLA (local) .fun(piece, ...)
6. | \-KEGGREST::keggList(database = category)
7. | \-KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
8. | \-httr::GET(url)
9. | \-httr:::request_perform(req, hu$handle$handle)
10. | +-httr:::request_fetch(req$output, req$url, handle)
11. | \-httr:::request_fetch.write_memory(req$output, req$url, handle)
12. | \-curl::curl_fetch_memory(url, handle = handle)
13. \-curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'zebrafish.Rmd' failed with diagnostics:
Timeout was reached [rest.kegg.jp]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
--- failed re-building ‘zebrafish.Rmd’
--- re-building ‘FELLA.Rnw’ using Sweave
Building through KEGGREST...
Error: processing vignette 'FELLA.Rnw' failed with diagnostics:
chunk 2 (label = 01_graph)
Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached [rest.kegg.jp]:
Connection timed out after 10002 milliseconds
--- failed re-building ‘FELLA.Rnw’
SUMMARY: processing the following files failed:
‘zebrafish.Rmd’ ‘FELLA.Rnw’
Error: Vignette re-building failed.
Execution halted