##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TAPseq
###
##############################################################################
##############################################################################


* checking for file ‘TAPseq/DESCRIPTION’ ... OK
* preparing ‘TAPseq’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘tapseq_primer_design.Rmd’ using rmarkdown
2025-12-15 23:40:43.129 R[92934:128572962] XType: com.apple.fonts is not accessible.
2025-12-15 23:40:43.130 R[92934:128572962] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘tapseq_primer_design.Rmd’

--- re-building ‘tapseq_target_genes.Rmd’ using rmarkdown
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Quitting from tapseq_target_genes.Rmd:54-59 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'tapseq_target_genes.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 ‘tapseq_target_genes.Rmd’

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

Error: Vignette re-building failed.
Execution halted