Error(s) in re-building vignettes:
--- re-building ‘DengueVignette.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.
Loading required package: ape
Loading required package: ade4
No protocol specified
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

   /// adegenet 2.1.1 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()



Attaching package: 'adegenet'

The following object is masked from 'package:phangorn':

    AICc

The following object is masked from 'package:treespace':

    .render.server.info

Quitting from lines 137-139 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘DengueVignette.Rmd’

--- re-building ‘TransmissionTreesVignette.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.
Loading required package: ape
Loading required package: ade4
No protocol specified
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

Attaching package: 'igraph'

The following objects are masked from 'package:ape':

    edges, mst, ring

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

--- finished re-building ‘TransmissionTreesVignette.Rmd’

--- re-building ‘introduction.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.
No protocol specified

   /// adegenet 2.1.1 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()



Attaching package: 'adegenet'

The following object is masked from 'package:treespace':

    .render.server.info


Attaching package: 'adegraphics'

The following objects are masked from 'package:ade4':

    kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
    s.label, s.logo, s.match, s.traject, s.value, table.value,
    triangle.class

The following object is masked from 'package:ape':

    zoom

Quitting from lines 138-139 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

--- re-building ‘tipCategories.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.
Loading required package: ape
Loading required package: ade4
No protocol specified
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
Loading required package: pander
--- finished re-building ‘tipCategories.Rmd’

SUMMARY: processing the following files failed:
  ‘DengueVignette.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted