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###
### Running command:
###
###   chmod a+r coMET -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data coMET
###
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##############################################################################


* checking for file 'coMET/DESCRIPTION' ... OK
* preparing 'coMET':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'coMET.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.
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.
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
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.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
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 "coMET.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 'coMET.Rnw' failed with diagnostics:
running 'texi2dvi' on 'coMET.tex' failed

LaTeX errors:
/coMET.tex:80: Package xcolor Error: Undefined color `fgcolor'.

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

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:141: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:158: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:212: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:225: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:238: Package xcolor Error: Undefined color `fgcolor'.

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

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:299: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:363: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:430: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:487: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:503: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:583: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:627: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:647: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:696: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:713: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:749: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:767: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:802: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:830: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:917: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:936: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:1162: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:1198: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:1220: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:1241: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:1256: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:1279: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:1309: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:1342: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:1362: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:1386: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:1398: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:1433: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:1468: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:1507: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
/coMET.tex:1561: Package xcolor Error: Undefined color `fgcolor'.

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

SUMMARY: processing the following file failed:
  'coMET.Rnw'

Error: Vignette re-building failed.
Execution halted