Multiple platform build/check report for BioC 3.21 - BUILD results for UniProt.ws on nebbiolo1

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
palomino7	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4566
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4604
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4545
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*

BUILD results for UniProt.ws on nebbiolo1

To the developers/maintainers of the UniProt.ws package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/UniProt.ws.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.

raw results

Summary

Package: UniProt.ws

Version: 2.48.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data UniProt.ws

StartedAt: 2025-08-13 19:41:20 -0400 (Wed, 13 Aug 2025)

EndedAt: 2025-08-13 19:41:51 -0400 (Wed, 13 Aug 2025)

EllapsedTime: 31.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data UniProt.ws
###
##############################################################################
##############################################################################


* checking for file ‘UniProt.ws/DESCRIPTION’ ... OK
* preparing ‘UniProt.ws’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘UniProt.ws.Rmd’ using rmarkdown

Quitting from UniProt.ws.Rmd:65-67 [availSpecies]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [ftp.uniprot.org]:
SSL connection timeout
---
Backtrace:
     ▆
  1. ├─UniProt.ws::availableUniprotSpecies(pattern = "musculus")
  2. │ └─UniProt.ws:::digestspecfile()
  3. │   └─UniProt.ws:::.getSpecfile(specfile)
  4. │     ├─BiocFileCache::bfcneedsupdate(bfc, names(rpath))
  5. │     └─BiocFileCache::bfcneedsupdate(bfc, names(rpath))
  6. │       └─base::vapply(rids, helper, logical(1), x = x)
  7. │         └─BiocFileCache (local) FUN(X[[i]], ...)
  8. │           └─BiocFileCache:::.httr_get_cache_info(fpath)
  9. │             ├─base::withCallingHandlers(...)
 10. │             └─httr::HEAD(link)
 11. │               └─httr:::request_perform(req, hu$handle$handle)
 12. │                 ├─httr:::request_fetch(req$output, req$url, handle)
 13. │                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 14. │                   └─curl::curl_fetch_memory(url, handle = handle)
 15. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'UniProt.ws.Rmd' failed with diagnostics:
Timeout was reached [ftp.uniprot.org]:
SSL connection timeout
--- failed re-building ‘UniProt.ws.Rmd’

SUMMARY: processing the following file failed:
  ‘UniProt.ws.Rmd’

Error: Vignette re-building failed.
Execution halted