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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 nipalsMCIA
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* checking for file ‘nipalsMCIA/DESCRIPTION’ ... OK
* preparing ‘nipalsMCIA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Analysis-of-MCIA-Decomposition.Rmd’ using rmarkdown
--- finished re-building ‘Analysis-of-MCIA-Decomposition.Rmd’

--- re-building ‘Predicting-New-Scores.Rmd’ using rmarkdown
--- finished re-building ‘Predicting-New-Scores.Rmd’

--- re-building ‘Single-Cell-Analysis.Rmd’ using rmarkdown

Quitting from Single-Cell-Analysis.Rmd:833-845 [seurat-markers-dot-adt]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'x' in selecting a method for function 'rownames': 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. ├─Seurat::DotPlot(...)
  2. ├─BiocGenerics::rownames(...)
  3. ├─SeuratObject::GetAssayData(object = obj, assay = "ADT", slot = "counts")
  4. ├─SeuratObject:::GetAssayData.Seurat(...)
  5. │ └─SeuratObject::.Deprecate(...)
  6. │   └─lifecycle::deprecate_stop(...)
  7. │     └─lifecycle:::deprecate_stop0(msg)
  8. │       └─rlang::cnd_signal(...)
  9. │         └─rlang:::signal_abort(cnd)
 10. │           └─base::signalCondition(cnd)
 11. └─base (local) `<fn>`(`<lfcycl__>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Single-Cell-Analysis.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'rownames': 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 ‘Single-Cell-Analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘Single-Cell-Analysis.Rmd’

Error: Vignette re-building failed.
Execution halted