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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 SpatialDecon
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* checking for file ‘SpatialDecon/DESCRIPTION’ ... OK
* preparing ‘SpatialDecon’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘SpatialDecon_vignette.Rmd’ using rmarkdown
2026-01-04 17:43:15.584 R[6859:627952592] XType: Using static font registry.

Quitting from SpatialDecon_vignette.Rmd:207-239 [createSeuratmatrix]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/lifecycle_error_deprecated>
Error:
! 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. ├─SpatialDecon::create_profile_matrix(...)
 2. ├─Seurat::GetAssayData(object = seuratObject, assay = "RNA", slot = "counts")
 3. └─SeuratObject:::GetAssayData.Seurat(...)
 4.   └─SeuratObject::.Deprecate(...)
 5.     └─lifecycle::deprecate_stop(...)
 6.       └─lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SpatialDecon_vignette.Rmd' failed with diagnostics:
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 ‘SpatialDecon_vignette.Rmd’

--- re-building ‘SpatialDecon_vignette_NSCLC.Rmd’ using rmarkdown
--- finished re-building ‘SpatialDecon_vignette_NSCLC.Rmd’

SUMMARY: processing the following file failed:
  ‘SpatialDecon_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted