Build/check report for BioC 3.22 - BUILD results for factR on nebbiolo2

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"	4888
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BUILD results for factR on nebbiolo2

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

Version: 1.12.0

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

StartedAt: 2026-02-03 17:19:19 -0500 (Tue, 03 Feb 2026)

EndedAt: 2026-02-03 17:19:44 -0500 (Tue, 03 Feb 2026)

EllapsedTime: 25.0 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 factR
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* checking for file ‘factR/DESCRIPTION’ ... OK
* preparing ‘factR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘factR.Rmd’ using rmarkdown

Quitting from factR.Rmd:167-169 [plottranscripts]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'args' in selecting a method for function 'do.call': `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `arrange()` instead.
ℹ See vignette('programming') for more help
---
Backtrace:
     ▆
  1. ├─factR::viewTranscripts(custom.gtf, "Zfr")
  2. │ ├─BiocGenerics::do.call(...)
  3. │ └─base::lapply(...)
  4. │   └─factR (local) FUN(X[[i]], ...)
  5. │     ├─base::suppressWarnings(...)
  6. │     │ └─base::withCallingHandlers(...)
  7. │     └─wiggleplotr::plotTranscripts(...)
  8. │       └─wiggleplotr:::plotTranscriptStructure(...)
  9. │         └─... %>% dplyr::filter(row_number() == 1)
 10. ├─dplyr::filter(., row_number() == 1)
 11. ├─dplyr::arrange_(., "transcript_id", "start")
 12. │ └─dplyr:::lazy_defunct("arrange")
 13. │   └─lifecycle::deprecate_stop(...)
 14. │     └─lifecycle:::deprecate_stop0(msg)
 15. │       └─rlang::cnd_signal(...)
 16. │         └─rlang:::signal_abort(cnd)
 17. │           └─base::signalCondition(cnd)
 18. └─base (local) `<fn>`(`<lfcycl__>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'factR.Rmd' failed with diagnostics:
error in evaluating the argument 'args' in selecting a method for function 'do.call': `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `arrange()` instead.
ℹ See vignette('programming') for more help
--- failed re-building ‘factR.Rmd’

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

Error: Vignette re-building failed.
Execution halted