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### Running command:
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###   chmod a+r TPP -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data TPP
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* checking for file 'TPP/DESCRIPTION' ... OK
* preparing 'TPP':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'NPARC_analysis_of_TPP_TR_data.Rnw' using knitr
texify: major issue: User/administrator updates are out-of-sync.
--- finished re-building 'NPARC_analysis_of_TPP_TR_data.Rnw'

--- re-building 'TPP_introduction_1D.Rnw' using knitr
texify: major issue: User/administrator updates are out-of-sync.
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "TPP_introduction_1D.tex" --max-iterations=20 -I "F:/biocbuild/bbs-3.20-bioc/R/share/texmf/tex/latex" -I "F:/biocbuild/bbs-3.20-bioc/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'TPP_introduction_1D.Rnw' failed with diagnostics:
running 'texi2dvi' on 'TPP_introduction_1D.tex' failed

LaTeX errors:
PP_introduction_1D.tex:78: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_1D.tex:90: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_1D.tex:140: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_1D.tex:159: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_1D.tex:172: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_1D.tex:203: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_1D.tex:218: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:237: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:274: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:291: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:330: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:343: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:368: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:432: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:475: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:497: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:615: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:625: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:642: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:674: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:690: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:729: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:762: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:774: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:789: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:832: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:843: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:858: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:872: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:890: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:923: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:937: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:952: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:961: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_1D.tex:1003: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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--- failed re-building 'TPP_introduction_1D.Rnw'

--- re-building 'TPP_introduction_2D.Rnw' using knitr
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
texify: major issue: User/administrator updates are out-of-sync.
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "TPP_introduction_2D.tex" --max-iterations=20 -I "F:/biocbuild/bbs-3.20-bioc/R/share/texmf/tex/latex" -I "F:/biocbuild/bbs-3.20-bioc/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'TPP_introduction_2D.Rnw' failed with diagnostics:
running 'texi2dvi' on 'TPP_introduction_2D.tex' failed

LaTeX errors:
PP_introduction_2D.tex:95: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_2D.tex:107: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_2D.tex:150: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_2D.tex:163: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_2D.tex:218: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_2D.tex:237: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_2D.tex:415: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_2D.tex:479: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_2D.tex:489: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_2D.tex:529: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_2D.tex:577: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_2D.tex:587: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_2D.tex:595: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_2D.tex:618: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_2D.tex:634: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_2D.tex:644: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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PP_introduction_2D.tex:657: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_2D.tex:690: Package xcolor Error: Undefined color `fgcolor'.

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PP_introduction_2D.tex:722: Package xcolor Error: Undefined color `fgcolor'.

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--- failed re-building 'TPP_introduction_2D.Rnw'

SUMMARY: processing the following files failed:
  'TPP_introduction_1D.Rnw' 'TPP_introduction_2D.Rnw'

Error: Vignette re-building failed.
Execution halted