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

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

--- re-building ‘maftools.Rmd’ using rmarkdown
Capture size [TCGA]:  35.8
Capture size [Input]: 50
Performing pairwise t-test for differences in mutation burden (per MB)..
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "axes" is not a graphical parameter
Estimating background scores from synonymous variants..
Not enough genes to build background. Using predefined values. (Mean = 0.279; SD = 0.13)
Estimating cluster scores from non-syn variants..
Comapring with background model and estimating p-values..
Done !
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "axes" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "axes" is not a graphical parameter
Gene: PML
9 transcripts available. Use arguments refSeqID or proteinID to manually specify tx name.
Using longer transcript NM_033238 for now.
9 transcripts available. Use arguments refSeqID or proteinID to manually specify tx name.
Using longer transcript NM_033238 for now.
Quitting from lines 482-485 (maftools.Rmd) 
Error: processing vignette 'maftools.Rmd' failed with diagnostics:
there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
--- failed re-building ‘maftools.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted