Error(s) in re-building vignettes:
--- re-building ‘PlotHaploNet.Rnw’ using Sweave
Loading required package: ape
Registered S3 method overwritten by 'pegas':
  method      from
  print.amova ade4

Attaching package: ‘pegas’

The following object is masked from ‘package:ape’:

    mst

Error: processing vignette 'PlotHaploNet.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'PlotHaploNet.tex' failed.
LaTeX errors:
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
--- failed re-building ‘PlotHaploNet.Rnw’

--- re-building ‘ReadingFiles.Rnw’ using Sweave
Error: processing vignette 'ReadingFiles.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'ReadingFiles.tex' failed.
LaTeX errors:
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
--- failed re-building ‘ReadingFiles.Rnw’

SUMMARY: processing the following files failed:
  ‘PlotHaploNet.Rnw’ ‘ReadingFiles.Rnw’

Error: Vignette re-building failed.
Execution halted