Multiple platform build/check report for BioC 3.22 - BUILD results for geva on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4824
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4615
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4562
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4541
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 kjohnson3

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.

raw results

Summary

Package: geva

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data geva

StartedAt: 2025-08-29 16:29:41 -0400 (Fri, 29 Aug 2025)

EndedAt: 2025-08-29 16:30:19 -0400 (Fri, 29 Aug 2025)

EllapsedTime: 38.4 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/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
2025-08-29 16:29:45.199 R[37595:121663711] XType: Using static font registry.
INFO - This is Biber 2.19
INFO - Logfile is 'geva.blg'
INFO - Reading 'geva.bcf'
INFO - Found 4 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex file 'references.bib' for section 0
INFO - LaTeX decoding ...
INFO - Found BibTeX data source 'references.bib'
Warning: LaTeX Warning: Citation 'smyth2005limma' on page 2 undefined on input line 164.
Warning: LaTeX Warning: Citation 'love2014moderated' on page 2 undefined on input line 1
Warning: 65.
Warning: LaTeX Warning: Citation 'nunes2018gene' on page 2 undefined on input line 168.
Warning: LaTeX Warning: Citation 'kallio2011chipster' on page 2 undefined on input line 
Warning: 169.
Warning: Package longtable Warning: Column widths have changed
Warning: (longtable)                in table 1 on input line 881.
Warning: Package longtable Warning: Column widths have changed
Warning: (longtable)                in table 2 on input line 920.
Warning: LaTeX Warning: Empty bibliography on input line 970.
Warning: Package longtable Warning: Table widths have changed. Rerun LaTeX.
Warning: LaTeX Warning: There were undefined references.
Warning: LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
Warning: Package biblatex Warning: Please (re)run Biber on the file:
Warning: (biblatex)                geva
Warning: (biblatex)                and rerun LaTeX afterwards.
Error: processing vignette 'geva.Rmd' failed with diagnostics:
Failed to build the bibliography via biber
--- failed re-building ‘geva.Rmd’

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

Error: Vignette re-building failed.
Execution halted