############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Hiiragi2013 ### ############################################################################## ############################################################################## * checking for file ‘Hiiragi2013/DESCRIPTION’ ... OK * preparing ‘Hiiragi2013’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘Hiiragi2013.Rnw’ using Sweave Loading required package: affy Loading required package: BiocGenerics Loading required package: generics Attaching package: ‘generics’ The following objects are masked from ‘package:base’: as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: boot Loading required package: clue Loading required package: cluster Loading required package: genefilter Loading required package: geneplotter Loading required package: lattice Attaching package: ‘lattice’ The following object is masked from ‘package:boot’: melanoma Loading required package: annotate Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: XML Loading required package: gplots Attaching package: ‘gplots’ The following object is masked from ‘package:IRanges’: space The following object is masked from ‘package:S4Vectors’: space The following object is masked from ‘package:stats’: lowess Loading required package: gtools Attaching package: ‘gtools’ The following objects are masked from ‘package:boot’: inv.logit, logit Loading required package: KEGGREST Loading required package: MASS Attaching package: ‘MASS’ The following object is masked from ‘package:AnnotationDbi’: select The following object is masked from ‘package:genefilter’: area Loading required package: mouse4302.db Loading required package: org.Mm.eg.db Loading required package: RColorBrewer Loading required package: xtable Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘mouse4302cdf’ Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘mouse4302cdf’ Error: processing vignette 'Hiiragi2013.Rnw' failed with diagnostics: Running 'texi2dvi' on 'Hiiragi2013.tex' failed. LaTeX errors: ! Package xcolor Error: Undefined color `Gray'. See the xcolor package documentation for explanation. Type H for immediate help. ... ! Emergency stop. ... l.1 library(" affy") ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘Hiiragi2013.Rnw’ SUMMARY: processing the following file failed: ‘Hiiragi2013.Rnw’ Error: Vignette re-building failed. Execution halted