Build/check report for BioC 3.21 experimental data - BUILD results for NanoporeRNASeq on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4827
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 NanoporeRNASeq on nebbiolo1

To the developers/maintainers of the NanoporeRNASeq package:
- 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: NanoporeRNASeq

Version: 1.18.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data NanoporeRNASeq

StartedAt: 2025-09-16 11:30:33 -0400 (Tue, 16 Sep 2025)

EndedAt: 2025-09-16 11:31:08 -0400 (Tue, 16 Sep 2025)

EllapsedTime: 34.8 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data NanoporeRNASeq
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* checking for file ‘NanoporeRNASeq/DESCRIPTION’ ... OK
* preparing ‘NanoporeRNASeq’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘NanoporeRNASeq.Rmd’ using rmarkdown

Quitting from NanoporeRNASeq.Rmd:58-71 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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. ├─ggplot2::autoplot(range, aes(col = strand), group.selfish = TRUE)
  2. └─ggbio::autoplot(range, aes(col = strand), group.selfish = TRUE)
  3.   └─ggbio (local) .local(object, ...)
  4.     ├─BiocGenerics::do.call(ggplot, c(list(data = object), list(aes.res)))
  5.     ├─base::do.call(ggplot, c(list(data = object), list(aes.res)))
  6.     ├─ggplot2 (local) `<fn>`(data = `<GRanges>`, `<ggplt2::>`)
  7.     └─ggbio:::ggplot.Vector(data = `<GRanges>`, `<ggplt2::>`)
  8.       └─ggbio::GGbio(gg, data = data)
  9.         ├─BiocGenerics::do.call(...)
 10.         ├─base::do.call(...)
 11.         └─methods (local) `<fn>`(...)
 12.           ├─methods::initialize(value, ...)
 13.           └─methods::initialize(value, ...)
 14.             └─methods::validObject(.Object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'NanoporeRNASeq.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 ‘NanoporeRNASeq.Rmd’

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

Error: Vignette re-building failed.
Execution halted