Build/check report for BioC 3.23 - BUILD results for genomation 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"	4823
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BUILD results for genomation on nebbiolo1

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

Version: 1.43.0

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

StartedAt: 2025-11-11 17:47:28 -0500 (Tue, 11 Nov 2025)

EndedAt: 2025-11-11 17:49:39 -0500 (Tue, 11 Nov 2025)

EllapsedTime: 130.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data genomation
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* checking for file ‘genomation/DESCRIPTION’ ... OK
* preparing ‘genomation’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘GenomationManual.Rmd’ using rmarkdown
Could not fetch https://raw.githubusercontent.com/BIMSBbioinfo/genomation/master/vignettes/Figures/multiHeatMatrix2-1.png
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/BIMSBbioinfo/genomation/master/vignettes/Figures/multiHeatMatrix2-1.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HandshakeFailed (Error_Misc "Network.Socket.recvBuf: resource vanished (Connection reset by peer)")))
Error: processing vignette 'GenomationManual.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘GenomationManual.Rmd’

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

Error: Vignette re-building failed.
Execution halted