############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r SCnorm -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data SCnorm ### ############################################################################## ############################################################################## * checking for file 'SCnorm/DESCRIPTION' ... OK * preparing 'SCnorm': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'SCnorm.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. Error in parse(text = code, keep.source = FALSE) : :12:19: unexpected symbol 11: PrintProgressPlots = TRUE 12: FilterCellNum ^ Warning in highr::hilight(x, format, prompt = options$prompt, markup = opts$markup) : the syntax of the source code is invalid; the fallback mode is used 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 "SCnorm.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 'SCnorm.Rnw' failed with diagnostics: running 'texi2dvi' on 'SCnorm.tex' failed LaTeX errors: s/SCnorm.tex:82: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:101: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:115: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:136: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:163: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:172: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:185: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:224: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:279: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:355: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:418: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:432: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:456: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:510: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:533: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:554: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:605: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:630: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:664: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:695: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:725: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:745: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:849: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... s/SCnorm.tex:890: Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... --- failed re-building 'SCnorm.Rnw' SUMMARY: processing the following file failed: 'SCnorm.Rnw' Error: Vignette re-building failed. Execution halted