Sergio Picart-Armada
| Snapshot Date: 2025-08-28 13:40 -0400 (Thu, 28 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/FELLA |
| git_branch: RELEASE_3_21 |
| git_last_commit: 9037a05 |
| git_last_commit_date: 2025-04-15 11:19:30 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-01 11:42 -0400 (Mon, 01 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
| 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 722/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FELLA 1.28.0 (landing page) Sergio Picart-Armada
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | 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: 1.28.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data FELLA |
| StartedAt: 2025-08-29 00:46:06 -0000 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 01:07:14 -0000 (Fri, 29 Aug 2025) |
| EllapsedTime: 1268.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data FELLA
###
##############################################################################
##############################################################################
* 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
Quitting from musmusculus.Rmd:74-84 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [rest.kegg.jp]: Send failure: Broken pipe
---
Backtrace:
x
1. +-KEGGREST::keggLink("enzyme", "mmu")
2. | \-KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
3. | \-httr::GET(url)
4. | \-httr:::request_perform(req, hu$handle$handle)
5. | +-httr:::request_fetch(req$output, req$url, handle)
6. | \-httr:::request_fetch.write_memory(req$output, req$url, handle)
7. | \-curl::curl_fetch_memory(url, handle = handle)
8. \-curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'musmusculus.Rmd' failed with diagnostics:
Timeout was reached [rest.kegg.jp]: Send failure: Broken pipe
--- failed 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]: Connection timed out after 10002 milliseconds
---
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>`(1L)
5. | \-FELLA (local) .fun(piece, ...)
6. | \-KEGGREST::keggList(database = category, organism = organism)
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]: Connection timed out after 10002 milliseconds
--- 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:
‘musmusculus.Rmd’ ‘zebrafish.Rmd’ ‘FELLA.Rnw’
Error: Vignette re-building failed.
Execution halted