Multiple platform build/check report for BioC 3.23 - BUILD results for dmGsea on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4829
lconway	macOS 12.7.6 Monterey	x86_64	R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"	4605
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4568
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 dmGsea on nebbiolo1

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

Version: 1.1.1

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data dmGsea

StartedAt: 2025-11-23 17:21:28 -0500 (Sun, 23 Nov 2025)

EndedAt: 2025-11-23 17:22:48 -0500 (Sun, 23 Nov 2025)

EllapsedTime: 80.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data dmGsea
###
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* checking for file ‘dmGsea/DESCRIPTION’ ... OK
* preparing ‘dmGsea’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘dmGsea.Rmd’ using rmarkdown

Quitting from dmGsea.Rmd:58-76 [example1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [rest.kegg.jp]:
SSL connection timeout
---
Backtrace:
     ▆
  1. ├─dmGsea::gsGene(...)
  2. │ └─dmGsea:::processGeneSets(geneSet, gset1, gset2, species, unique(names(genep)))
  3. │   └─dmGsea::getKEGG(species)
  4. │     └─KEGGREST::keggLink("pathway", species)
  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 'dmGsea.Rmd' failed with diagnostics:
Timeout was reached [rest.kegg.jp]:
SSL connection timeout
--- failed re-building ‘dmGsea.Rmd’

SUMMARY: processing the following file failed:
  ‘dmGsea.Rmd’

Error: Vignette re-building failed.
Execution halted