Multiple platform build/check report for BioC 3.20 - BUILD results for genomation on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4753
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4501
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4524
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4476
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4407
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 genomation on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: genomation

Version: 1.38.0

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

StartedAt: 2025-02-03 23:48:50 -0000 (Mon, 03 Feb 2025)

EndedAt: 2025-02-03 23:50:52 -0000 (Mon, 03 Feb 2025)

EllapsedTime: 122.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/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 to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GenomationManual.Rmd’ using rmarkdown
Could not fetch https://raw.githubusercontent.com/BIMSBbioinfo/genomation/master/vignettes/Figures/heatMatrixScales-1.png
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/BIMSBbioinfo/genomation/master/vignettes/Figures/heatMatrixScales-1.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 ConnectionTimeout
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