Multiple platform build/check report for BioC 3.22 - BUILD results for fgsea on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4882
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4673
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4607
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4671
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 fgsea on kjohnson1

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

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data fgsea

StartedAt: 2025-12-16 00:21:27 -0500 (Tue, 16 Dec 2025)

EndedAt: 2025-12-16 00:28:48 -0500 (Tue, 16 Dec 2025)

EllapsedTime: 441.4 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data fgsea
###
##############################################################################
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* checking for file ‘fgsea/DESCRIPTION’ ... OK
* preparing ‘fgsea’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘fgsea-tutorial.Rmd’ using rmarkdown
2025-12-16 00:22:27.080 R[15244:283755877] XType: Using static font registry.
--- finished re-building ‘fgsea-tutorial.Rmd’

--- re-building ‘geseca-tutorial.Rmd’ using rmarkdown

Quitting from geseca-tutorial.Rmd:349-369 [unnamed-chunk-26]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SpatialPlot()`:
! Please run `UpdateSeuratObject` on your Seurat object first to ensure that data aligns to the image slice1 when plotting.
---
Backtrace:
    ▆
 1. └─fgsea::plotCoregulationProfileSpatial(...)
 2.   └─base::lapply(...)
 3.     └─fgsea (local) FUN(X[[i]], ...)
 4.       └─fgsea::plotCoregulationProfileSpatial(...)
 5.         └─Seurat::SpatialFeaturePlot(...)
 6.           └─Seurat::SpatialPlot(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'geseca-tutorial.Rmd' failed with diagnostics:
Please run `UpdateSeuratObject` on your Seurat object first to ensure that data aligns to the image slice1 when plotting.
--- failed re-building ‘geseca-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘geseca-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted