| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-12-13 11:47 -0500 (Sat, 13 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" | 4874 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R 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 304/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CelliD 1.19.0 (landing page) Akira Cortal
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the CelliD package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CelliD.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: CelliD |
| Version: 1.19.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CelliD |
| StartedAt: 2025-12-12 15:51:10 -0500 (Fri, 12 Dec 2025) |
| EndedAt: 2025-12-12 15:52:42 -0500 (Fri, 12 Dec 2025) |
| EllapsedTime: 92.0 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 CelliD
###
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* checking for file ‘CelliD/DESCRIPTION’ ... OK
* preparing ‘CelliD’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to process help pages)
* saving partial Rd database
* creating vignettes ... ERROR
--- re-building ‘BioconductorVignette.Rmd’ using rmarkdown
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Quitting from BioconductorVignette.Rmd:97-99 [MCA1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'x' in selecting a method for function 'as.matrix': The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
---
Backtrace:
▆
1. ├─CelliD::RunMCA(Baron)
2. ├─CelliD:::RunMCA.Seurat(Baron)
3. │ ├─base::as.matrix(GetAssayData(X, slot = slot))
4. │ ├─SeuratObject::GetAssayData(X, slot = slot)
5. │ └─SeuratObject:::GetAssayData.Seurat(X, slot = slot)
6. │ └─SeuratObject::.Deprecate(...)
7. │ └─lifecycle::deprecate_stop(...)
8. │ └─lifecycle:::deprecate_stop0(msg)
9. │ └─rlang::cnd_signal(...)
10. │ └─rlang:::signal_abort(cnd)
11. │ └─base::signalCondition(cnd)
12. └─base (local) `<fn>`(`<lfcycl__>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'BioconductorVignette.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.matrix': The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
--- failed re-building ‘BioconductorVignette.Rmd’
SUMMARY: processing the following file failed:
‘BioconductorVignette.Rmd’
Error: Vignette re-building failed.
Execution halted