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

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

Version: 1.15.02

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

StartedAt: 2025-10-23 19:11:53 -0400 (Thu, 23 Oct 2025)

EndedAt: 2025-10-23 19:12:42 -0400 (Thu, 23 Oct 2025)

EllapsedTime: 49.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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

--- re-building ‘infer_species.Rmd’ using rmarkdown
--- finished re-building ‘infer_species.Rmd’

--- re-building ‘orthogene.Rmd’ using rmarkdown

-- zebrafish

Quitting from orthogene.Rmd:146-153 [map_genes]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `gprofiler_request()`:
! There's an issue with your request to g:Profiler.
Error code: 503.
Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
---
Backtrace:
    ▆
 1. └─orthogene::map_genes(genes = genes, species = "mouse", drop_na = FALSE)
 2.   └─gprofiler2::gconvert(...)
 3.     └─gprofiler2:::gprofiler_request(url, body)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'orthogene.Rmd' failed with diagnostics:
There's an issue with your request to g:Profiler.
Error code: 503.
Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
--- failed re-building ‘orthogene.Rmd’

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

Error: Vignette re-building failed.
Execution halted