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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 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