Error(s) in re-building vignettes:
--- re-building 'DrawingPhylogenies.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 "DrawingPhylogenies.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 'DrawingPhylogenies.Rnw' failed with diagnostics:
running 'texi2dvi' on 'DrawingPhylogenies.tex' failed

LaTeX errors:
genies.tex:14: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:60: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:70: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:85: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:141: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:153: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:175: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:254: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:261: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:280: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:303: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:317: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:325: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:332: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:356: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:423: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:434: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:440: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:456: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:468: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:486: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:514: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:520: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:566: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:585: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:605: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:622: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:632: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:642: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:664: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:695: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:718: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:739: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:764: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:772: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:831: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:841: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:850: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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genies.tex:868: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
Type  H <return>  for im
--- failed re-building 'DrawingPhylogenies.Rnw'

--- re-building 'MoranI.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 "MoranI.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
--- finished re-building 'MoranI.Rnw'

--- re-building 'RandomTopologies.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 "RandomTopologies.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 'RandomTopologies.Rnw' failed with diagnostics:
running 'texi2dvi' on 'RandomTopologies.tex' failed

LaTeX errors:
gies.tex:13: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:48: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:74: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:87: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:104: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:122: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:151: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:162: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:174: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:193: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:204: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:232: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:249: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:261: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:280: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:294: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:302: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:374: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:413: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:421: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:433: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:495: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:508: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:527: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:559: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:621: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:632: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:640: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:689: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:700: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:712: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:729: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:759: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:792: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:799: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:864: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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gies.tex:873: Package xcolor Error: Undefined color `darkblue'.

See the xcolor package documentation for explanation.
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--- failed re-building 'RandomTopologies.Rnw'

SUMMARY: processing the following files failed:
  'DrawingPhylogenies.Rnw' 'RandomTopologies.Rnw'

Error: Vignette re-building failed.
Execution halted