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This page was generated on 2025-12-16 11:35 -0500 (Tue, 16 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4875
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4583
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 2183/2332HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tidybulk 2.1.0  (landing page)
Stefano Mangiola
Snapshot Date: 2025-12-15 13:40 -0500 (Mon, 15 Dec 2025)
git_url: https://git.bioconductor.org/packages/tidybulk
git_branch: devel
git_last_commit: 903ed2a
git_last_commit_date: 2025-10-29 10:57:24 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for tidybulk on nebbiolo1

To the developers/maintainers of the tidybulk package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tidybulk.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: tidybulk
Version: 2.1.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data tidybulk
StartedAt: 2025-12-15 20:19:04 -0500 (Mon, 15 Dec 2025)
EndedAt: 2025-12-15 20:33:09 -0500 (Mon, 15 Dec 2025)
EllapsedTime: 844.9 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data tidybulk
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* checking for file ‘tidybulk/DESCRIPTION’ ... OK
* preparing ‘tidybulk’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to process help pages)
* creating vignettes ... ERROR
--- re-building ‘comparison_coding.Rmd’ using rmarkdown
--- finished re-building ‘comparison_coding.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning: ggrepel: 15750 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 15790 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 15780 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 15789 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 15790 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 784 unlabeled data points (too many overlaps). Consider increasing max.overlaps

Quitting from introduction.Rmd:937-953 [enrichment-gene-rank-analysis]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
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Error: processing vignette 'introduction.Rmd' failed with diagnostics:
The packages "clusterProfiler" and "enrichplot" are required.
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted