############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Category ### ############################################################################## ############################################################################## * checking for file ‘Category/DESCRIPTION’ ... OK * preparing ‘Category’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘Category.Rnw’ using Sweave 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. 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: org.Hs.eg.db Loading required package: Matrix Attaching package: ‘Matrix’ The following object is masked from ‘package:S4Vectors’: expand Error: processing vignette 'Category.Rnw' failed with diagnostics: chunk 10 (label = KEGGmnplot) Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [rest.kegg.jp]: Connection timed out after 10003 milliseconds --- failed re-building ‘Category.Rnw’ --- re-building ‘ChromBand.Rnw’ using Sweave Loading required package: regioneR Loading required package: GenomicRanges Loading required package: Seqinfo Loading required package: lattice Attaching package: 'limma' The following object is masked from 'package:geneplotter': plotMA The following object is masked from 'package:BiocGenerics': plotMA Attaching package: 'graph' The following object is masked from 'package:XML': addNode --- finished re-building 'ChromBand.Rnw' SUMMARY: processing the following file failed: 'Category.Rnw' Error: Vignette re-building failed. Execution halted