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

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"	4882
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4673
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4607
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4671
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 SVP on taishan

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

Version: 1.2.1

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

StartedAt: 2025-12-16 06:58:57 -0000 (Tue, 16 Dec 2025)

EndedAt: 2025-12-16 07:04:32 -0000 (Tue, 16 Dec 2025)

EllapsedTime: 334.3 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 SVP
###
##############################################################################
##############################################################################


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

Quitting from SVP.Rmd:116-162 [Biocarta]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2024.1.Mm/m2.cp.biocarta.v2024.1.Mm.symbols.gmt'
---
Backtrace:
    ▆
 1. ├─SVP::runSGSA(...)
 2. └─SVP::runSGSA(...)
 3.   └─SVP:::.extract.gset(gset.idx.list, gene.name = symbol.from.gson)
 4.     └─SVP:::.read.gmt(x)
 5.       └─base::readLines(gmtfile)
 6.         └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SVP.Rmd' failed with diagnostics:
cannot open the connection to 'https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2024.1.Mm/m2.cp.biocarta.v2024.1.Mm.symbols.gmt'
--- failed re-building ‘SVP.Rmd’

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

Error: Vignette re-building failed.
Execution halted