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

Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "PlotHaploNet.tex" --max-iterations=20 -I "C:/r_packages/rinst/share/texmf/tex/latex" -I "C:/r_packages/rinst/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'PlotHaploNet.Rnw' failed with diagnostics:
running 'texi2dvi' on 'PlotHaploNet.tex' failed

LaTeX errors:
ploNet.tex:18: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:97: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:110: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:129: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:144: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:162: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:171: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:182: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:197: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:230: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:243: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:256: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:268: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:289: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:316: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:326: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:333: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:402: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:428: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:484: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:498: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:523: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:547: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:554: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:564: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
ploNet.tex:575: 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
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "ReadingFiles.tex" --max-iterations=20 -I "C:/r_packages/rinst/share/texmf/tex/latex" -I "C:/r_packages/rinst/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'ReadingFiles.Rnw' failed with diagnostics:
running 'texi2dvi' on 'ReadingFiles.tex' failed

LaTeX errors:
gFiles.tex:27: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:106: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:115: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:122: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:146: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:154: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:165: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:200: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:224: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:235: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:265: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:274: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:290: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:305: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:316: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:335: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:369: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:380: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:386: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:392: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:398: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:410: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:423: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:431: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:437: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:450: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:523: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:553: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:566: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:578: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
gFiles.tex:586: 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