Error(s) in re-building vignettes:
  ...
--- re-building ‘HaDeX.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 41-44 (HaDeX.Rmd) 
Error: processing vignette 'HaDeX.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘HaDeX.Rmd’

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

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

Attaching package: 'gridExtra'

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

    combine

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
--- finished re-building ‘mass_comparison.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

`summarise()` has grouped output by 'Sequence', 'Start', 'End'. You can override using the `.groups` argument.
`summarise()` has grouped output by 'Sequence', 'Start', 'End'. You can override using the `.groups` argument.
`summarise()` has grouped output by 'Sequence', 'Start'. You can override using the `.groups` argument.
--- finished re-building ‘transformation.Rmd’

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

Error: Vignette re-building failed.
Execution halted