Multiple platform build/check report for BioC 3.22 - BUILD results for methylGSA on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4796
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4536
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4578
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4519
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4517
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 methylGSA on taishan

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

Version: 1.27.0

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

StartedAt: 2025-08-01 01:02:09 -0000 (Fri, 01 Aug 2025)

EndedAt: 2025-08-01 01:13:58 -0000 (Fri, 01 Aug 2025)

EllapsedTime: 709.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data methylGSA
###
##############################################################################
##############################################################################


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

Quitting from methylGSA-vignette.Rmd:128-132 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! cannot read from connection
---
Backtrace:
    ▆
 1. └─methylGSA::methylglm(...)
 2.   └─methylGSA::getDescription(GSids = ID, GS.type = GS.type)
 3.     └─clusterProfiler::download_KEGG("hsa", keggType = "KEGG", keyType = "kegg")
 4.       └─clusterProfiler:::download.KEGG.Path(species)
 5.         └─clusterProfiler:::kegg_link(species, "pathway")
 6.           └─clusterProfiler:::kegg_rest(url)
 7.             └─yulab.utils::yread(rest_url)
 8.               ├─base::do.call(reader, args = c(file, params))
 9.               └─base (local) `<fn>`("https://rest.kegg.jp/link/hsa/pathway")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'methylGSA-vignette.Rmd' failed with diagnostics:
cannot read from connection
--- failed re-building ‘methylGSA-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘methylGSA-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted