Multiple platform build/check report for BioC 3.22 - BUILD results for scruff 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"	4719
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4538
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4522
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4543
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 scruff on nebbiolo2

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

Version: 1.27.0

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

StartedAt: 2025-09-14 19:52:00 -0400 (Sun, 14 Sep 2025)

EndedAt: 2025-09-14 19:53:48 -0400 (Sun, 14 Sep 2025)

EllapsedTime: 108.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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

Quitting from scruff.Rmd:218-227 [visualize_reads]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
---
Backtrace:
     ▆
  1. └─scruff::rview(bamExample, chr = "MT", start = start, end = end)
  2.   ├─ggplot2::ggplot(readsGr)
  3.   └─ggbio:::ggplot.Vector(readsGr)
  4.     └─ggbio::GGbio(gg, data = data)
  5.       ├─BiocGenerics::do.call(...)
  6.       ├─base::do.call(...)
  7.       └─methods (local) `<fn>`(...)
  8.         ├─methods::initialize(value, ...)
  9.         └─methods::initialize(value, ...)
 10.           └─methods::validObject(.Object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'scruff.Rmd' failed with diagnostics:
invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
--- failed re-building ‘scruff.Rmd’

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

Error: Vignette re-building failed.
Execution halted