Build/check report for BioC 3.22 - BUILD results for Doscheda on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4886
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BUILD results for Doscheda on nebbiolo2

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

Version: 1.32.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 Doscheda

StartedAt: 2026-01-26 17:32:14 -0500 (Mon, 26 Jan 2026)

EndedAt: 2026-01-26 17:32:55 -0500 (Mon, 26 Jan 2026)

EllapsedTime: 41.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 Doscheda
###
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* checking for file ‘Doscheda/DESCRIPTION’ ... OK
* preparing ‘Doscheda’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Doscheda.Rmd’ using rmarkdown

Quitting from Doscheda.Rmd:147-150 [fitModelEx]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.humanmine.org]:
SSL connection timeout
---
Backtrace:
     ▆
  1. ├─Doscheda::runNormalisation(ex)
  2. ├─Doscheda::runNormalisation(ex)
  3. │ └─Doscheda:::normalize_data(...)
  4. │   └─Doscheda:::uniprotGene(organism)
  5. │     └─httr::POST(...)
  6. │       └─httr:::request_perform(req, hu$handle$handle)
  7. │         ├─httr:::request_fetch(req$output, req$url, handle)
  8. │         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
  9. │           └─curl::curl_fetch_memory(url, handle = handle)
 10. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Doscheda.Rmd' failed with diagnostics:
Timeout was reached [www.humanmine.org]:
SSL connection timeout
--- failed re-building ‘Doscheda.Rmd’

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

Error: Vignette re-building failed.
Execution halted