| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-12-15 11:35 -0500 (Mon, 15 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R 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 729/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fgsea 1.37.2 (landing page) Alexey Sergushichev
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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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. |
| Package: fgsea |
| Version: 1.37.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data fgsea |
| StartedAt: 2025-12-14 16:21:38 -0500 (Sun, 14 Dec 2025) |
| EndedAt: 2025-12-14 16:24:31 -0500 (Sun, 14 Dec 2025) |
| EllapsedTime: 173.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /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 (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘fgsea-tutorial.Rmd’ using rmarkdown
2025-12-14 16:22:00.143 R[4889:390990174] 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