############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r ggbio -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ggbio ### ############################################################################## ############################################################################## * checking for file 'ggbio/DESCRIPTION' ... OK * preparing 'ggbio': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'ggbio.Rnw' using Sweave --- finished re-building 'ggbio.Rnw' cp realvignettes/*.Rnw . F:/biocbuild/bbs-3.20-bioc/R/bin/Rscript -e "library(knitr); knit2pdf('ggbio.Rnw')" processing file: ggbio.Rnw 1/125 2/125 [style-knitr] 3/125 4/125 [setup] 5/125 6/125 [citation] 7/125 8/125 [unnamed-chunk-1] 9/125 10/125 [unnamed-chunk-2] 11/125 12/125 [unnamed-chunk-3] 13/125 14/125 [unnamed-chunk-4] 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. 15/125 16/125 [unnamed-chunk-5] 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. 17/125 18/125 [unnamed-chunk-6] pdftex: major issue: User/administrator updates are out-of-sync. pdfcrop: major issue: User/administrator 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are out-of-sync. 109/125 110/125 [edit-space] pdftex: major issue: User/administrator updates are out-of-sync. pdfcrop: major issue: User/administrator updates are out-of-sync. 111/125 112/125 [unnamed-chunk-40] pdftex: major issue: User/administrator updates are out-of-sync. pdfcrop: major issue: User/administrator updates are out-of-sync. 113/125 114/125 [unnamed-chunk-41] 115/125 116/125 [unnamed-chunk-42] pdftex: major issue: User/administrator updates are out-of-sync. pdfcrop: major issue: User/administrator updates are out-of-sync. 117/125 118/125 [unnamed-chunk-43] 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. 119/125 120/125 [unnamed-chunk-44] 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. 121/125 122/125 [unnamed-chunk-45] 123/125 124/125 [session-info] 125/125 output file: ggbio.tex ! Package xcolor Error: Undefined color `fgcolor'. ! pdflatex: major issue: User/administrator updates are out-of-sync. Error: LaTeX failed to compile ggbio.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See ggbio.log for more info. Execution halted make: *** [Makefile:15: ggbio.pdf] Error 1 Error in tools::buildVignettes(dir = ".", tangle = TRUE) : running 'make' failed Execution halted