Multiple platform build/check report for BioC 3.22 - BUILD results for epigraHMM on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4898
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4688
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4634
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4658
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 epigraHMM on nebbiolo2

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

Version: 1.17.3

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

StartedAt: 2025-10-23 17:34:32 -0400 (Thu, 23 Oct 2025)

EndedAt: 2025-10-23 17:37:47 -0400 (Thu, 23 Oct 2025)

EllapsedTime: 195.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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

Quitting from epigraHMM.Rmd:140-157 [data_input_baminput]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [genome.ucsc.edu]:
SSL connection timeout
---
Backtrace:
     ▆
  1. ├─epigraHMM::epigraHMMDataSetFromBam(...)
  2. │ └─epigraHMM:::getGap(gapTrack, genome, genomeList[["seqinfo"]])
  3. │   ├─rtracklayer::browserSession()
  4. │   └─rtracklayer::browserSession()
  5. │     ├─rtracklayer::browserSession("UCSC", ...)
  6. │     └─rtracklayer::browserSession("UCSC", ...)
  7. │       └─methods::new(class, ...)
  8. │         ├─methods::initialize(value, ...)
  9. │         └─rtracklayer::initialize(value, ...)
 10. │           └─rtracklayer (local) .local(.Object, ...)
 11. │             └─httr::GET(gwURL, config)
 12. │               └─httr:::request_perform(req, hu$handle$handle)
 13. │                 ├─httr:::request_fetch(req$output, req$url, handle)
 14. │                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 15. │                   └─curl::curl_fetch_memory(url, handle = handle)
 16. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'epigraHMM.Rmd' failed with diagnostics:
Timeout was reached [genome.ucsc.edu]:
SSL connection timeout
--- failed re-building ‘epigraHMM.Rmd’

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

Error: Vignette re-building failed.
Execution halted