Multiple platform build/check report for BioC 3.21 - BUILD results for geva on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4658
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4455
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4408
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 geva on kunpeng2

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

Version: 1.15.0

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

StartedAt: 2025-01-24 23:16:17 -0000 (Fri, 24 Jan 2025)

EndedAt: 2025-01-24 23:18:47 -0000 (Fri, 24 Jan 2025)

EllapsedTime: 150.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data geva
###
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* checking for file ‘geva/DESCRIPTION’ ... OK
* preparing ‘geva’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘geva.Rmd’ using rmarkdown
Warning in Sys.setlocale("LC_TIME", "English_United States") :
  OS reports request to set locale to "English_United States" cannot be honored
! Missing $ inserted.
<inserted text> 
                $
l.412 ...e is applied using a threshold of (\alpha
                                                   \textless{} 

Try to find the following text in /home/biocbuild/tmp/Rtmpc0JpR7/Rbuildadac64ec63767/geva/vignettes/geva.Rmd:
  ...e is applied using a threshold of (\alpha 

You may need to add $ $ around a certain inline R expression `r ` in /home/biocbuild/tmp/Rtmpc0JpR7/Rbuildadac64ec63767/geva/vignettes/geva.Rmd (see the above hint). See https://github.com/rstudio/rmarkdown/issues/385 for more info.
Error: processing vignette 'geva.Rmd' failed with diagnostics:
LaTeX failed to compile /home/biocbuild/tmp/Rtmpc0JpR7/Rbuildadac64ec63767/geva/vignettes/geva.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See geva.log for more info.
--- failed re-building ‘geva.Rmd’

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

Error: Vignette re-building failed.
Execution halted