Error(s) in re-building vignettes:
--- re-building ‘PCMBase.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Failed with error:  'there is no package called 'ggtree''
trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/treeio_1.8.2.tgz'
Content type 'application/x-gzip' length 719329 bytes (702 KB)
==================================================
downloaded 702 KB

trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/BiocVersion_3.9.0.tgz'
Content type 'application/x-gzip' length 5513 bytes
==================================================
downloaded 5513 bytes

trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/ggtree_1.16.6.tgz'
Content type 'application/x-gzip' length 685419 bytes (669 KB)
==================================================
downloaded 669 KB

Quitting from lines 37-53 (PCMBase.Rmd) 
Error: processing vignette 'PCMBase.Rmd' failed with diagnostics:
argument is not interpretable as logical
--- failed re-building ‘PCMBase.Rmd’

--- re-building ‘PCMCreateModel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘PCMCreateModel.Rmd’

--- re-building ‘PCMParam.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘PCMParam.Rmd’

--- re-building ‘PCMTracePruning.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘PCMTracePruning.Rmd’

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

Error: Vignette re-building failed.
Execution halted