Build/check report for BioC 3.22 - BUILD results for GSEABenchmarkeR 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"	4890
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BUILD results for GSEABenchmarkeR on nebbiolo2

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

Version: 1.30.0

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

StartedAt: 2026-02-16 18:06:43 -0500 (Mon, 16 Feb 2026)

EndedAt: 2026-02-16 18:08:02 -0500 (Mon, 16 Feb 2026)

EllapsedTime: 79.1 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 GSEABenchmarkeR
###
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* checking for file ‘GSEABenchmarkeR/DESCRIPTION’ ... OK
* preparing ‘GSEABenchmarkeR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GSEABenchmarkeR.Rmd’ using rmarkdown

Quitting from GSEABenchmarkeR.Rmd:217-220 [rseqComp]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
     ▆
  1. └─GSEABenchmarkeR::loadEData("tcga", nr.datasets = 2)
  2.   └─GSEABenchmarkeR:::.loadTCGA(nr.datasets, cache, ...)
  3.     └─GSEABenchmarkeR:::.retrieveGSE62944FromEHub(with.clin.vars)
  4.       ├─base::suppressMessages(...)
  5.       │ └─base::withCallingHandlers(...)
  6.       └─ExperimentHub::ExperimentHub()
  7.         └─AnnotationHub::.Hub(...)
  8.           └─base::tryCatch(...)
  9.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11.                 └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'GSEABenchmarkeR.Rmd' failed with diagnostics:
failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘GSEABenchmarkeR.Rmd’

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

Error: Vignette re-building failed.
Execution halted