| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-13 12:03 -0400 (Sat, 13 Sep 2025).
| 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 | ||||
| Package 2262/2327 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| universalmotif 1.27.2 (landing page) Benjamin Jean-Marie Tremblay
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the universalmotif package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/universalmotif.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. |
| Package: universalmotif |
| Version: 1.27.2 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 universalmotif |
| StartedAt: 2025-09-12 20:31:43 -0400 (Fri, 12 Sep 2025) |
| EndedAt: 2025-09-12 20:35:44 -0400 (Fri, 12 Sep 2025) |
| EllapsedTime: 241.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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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 universalmotif
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* checking for file ‘universalmotif/DESCRIPTION’ ... OK
* preparing ‘universalmotif’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Introduction.Rmd’ using rmarkdown
--- finished re-building ‘Introduction.Rmd’
--- re-building ‘IntroductionToSequenceMotifs.Rmd’ using rmarkdown
--- finished re-building ‘IntroductionToSequenceMotifs.Rmd’
--- re-building ‘MotifComparisonAndPvalues.Rmd’ using rmarkdown
--- finished re-building ‘MotifComparisonAndPvalues.Rmd’
--- re-building ‘MotifManipulation.Rmd’ using rmarkdown
--- finished re-building ‘MotifManipulation.Rmd’
--- re-building ‘SequenceSearches.Rmd’ using rmarkdown
Quitting from SequenceSearches.Rmd:374-404 [unnamed-chunk-20]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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:
x
1. +-ggplot2::autoplot(...)
2. \-ggbio::autoplot(...)
3. \-ggbio (local) .local(object, ...)
4. \-ggbio::GGbio(p, data = object)
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 'SequenceSearches.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 ‘SequenceSearches.Rmd’
SUMMARY: processing the following file failed:
‘SequenceSearches.Rmd’
Error: Vignette re-building failed.
Execution halted