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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
2023-10-15 18:12:16.072 R[71367:970879370] XType: com.apple.fonts is not accessible.
2023-10-15 18:12:16.072 R[71367:970879370] XType: XTFontStaticRegistry is enabled.

Quitting from lines 97-121 [unnamed-chunk-4] (analysis_diff_meth.Rmd)
Error: processing vignette 'analysis_diff_meth.Rmd' failed with diagnostics:
bad value
--- failed 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

Quitting from lines 68-85 [unnamed-chunk-2] (analysis_motif_enrichment.Rmd)
Error: processing vignette 'analysis_motif_enrichment.Rmd' failed with diagnostics:
bad value
--- failed 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

Quitting from lines 246-294 [unnamed-chunk-8] (input.Rmd)
Error: processing vignette 'input.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': bad value
--- failed 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
--- finished re-building ‘plots_schematic.Rmd’

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

SUMMARY: processing the following files failed:
  ‘analysis_diff_meth.Rmd’ ‘analysis_motif_enrichment.Rmd’ ‘input.Rmd’

Error: Vignette re-building failed.
Execution halted