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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 ELMER
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* checking for file ‘ELMER/DESCRIPTION’ ... OK
* preparing ‘ELMER’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘analysis_data_input.Rmd’ using rmarkdown
--- finished re-building ‘analysis_data_input.Rmd’

--- re-building ‘analysis_diff_meth.Rmd’ using rmarkdown
2025-01-10 16:17:28.025 R[32166:275635672] XType: Using static font registry.
--- finished re-building ‘analysis_diff_meth.Rmd’

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

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

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

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

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

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

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

--- re-building ‘plots_TF.Rmd’ using rmarkdown
Warning: ggrepel: 66 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘plots_TF.Rmd’

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

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

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

--- re-building ‘plots_schematic.Rmd’ using rmarkdown

Quitting from lines 44-51 [unnamed-chunk-3] (plots_schematic.Rmd)
Error: processing vignette 'plots_schematic.Rmd' failed with diagnostics:
No method for subsetting an XMLInternalDocument with numeric
--- failed re-building ‘plots_schematic.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted