Back to Multiple platform build/check report for BioC 3.23:   simplified   long
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2025-12-13 11:46 -0500 (Sat, 13 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4874
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4582
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 1437/2332HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Nebulosa 1.21.0  (landing page)
Jose Alquicira-Hernandez
Snapshot Date: 2025-12-12 13:40 -0500 (Fri, 12 Dec 2025)
git_url: https://git.bioconductor.org/packages/Nebulosa
git_branch: devel
git_last_commit: 7bc1fc4
git_last_commit_date: 2025-10-29 11:01:25 -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 Nebulosa on nebbiolo1

To the developers/maintainers of the Nebulosa package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Nebulosa.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: Nebulosa
Version: 1.21.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Nebulosa
StartedAt: 2025-12-12 19:06:56 -0500 (Fri, 12 Dec 2025)
EndedAt: 2025-12-12 19:09:11 -0500 (Fri, 12 Dec 2025)
EllapsedTime: 134.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Nebulosa
###
##############################################################################
##############################################################################


* checking for file ‘Nebulosa/DESCRIPTION’ ... OK
* preparing ‘Nebulosa’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘introduction.Rmd’ using rmarkdown
--- finished re-building ‘introduction.Rmd’

--- re-building ‘nebulosa_seurat.Rmd’ using rmarkdown
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Quitting from nebulosa_seurat.Rmd:127-129 [plot_cd4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'nebulosa_seurat.Rmd' failed with diagnostics:
The `slot` argument of `FetchData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
--- failed re-building ‘nebulosa_seurat.Rmd’

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

Error: Vignette re-building failed.
Execution halted