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

Quitting from lines 141-155 [unnamed-chunk-6] (calculating_methylation_transcription_correlations.Rmd)
Error: processing vignette 'calculating_methylation_transcription_correlations.Rmd' failed with diagnostics:
unused arguments (expand_upstream = 5000, expand_downstream = 5000)
--- failed re-building ‘calculating_methylation_transcription_correlations.Rmd’

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

Quitting from lines 68-82 [unnamed-chunk-4] (identifying_tmrs.Rmd)
Error: processing vignette 'identifying_tmrs.Rmd' failed with diagnostics:
unused arguments (expand_upstream = 5000, expand_downstream = 5000)
--- failed re-building ‘identifying_tmrs.Rmd’

--- re-building ‘working_with_meth_rses.Rmd’ using rmarkdown
2024-10-09 17:42:23.065 R[60347:60546584] XType: Using static font registry.
--- finished re-building ‘working_with_meth_rses.Rmd’

SUMMARY: processing the following files failed:
  ‘calculating_methylation_transcription_correlations.Rmd’
  ‘identifying_tmrs.Rmd’

Error: Vignette re-building failed.
Execution halted