############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r QuartPAC -R && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data QuartPAC ### ############################################################################## ############################################################################## * checking for file 'QuartPAC/DESCRIPTION' ... OK * preparing 'QuartPAC': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'QuartPAC.Rnw' using Sweave Loading required package: iPAC Loading required package: gdata gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED. gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED. Attaching package: 'gdata' The following object is masked from 'package:stats': nobs The following object is masked from 'package:utils': object.size The following object is masked from 'package:base': startsWith Loading required package: scatterplot3d Loading required package: Biostrings Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from 'package:gdata': combine 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, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:gdata': first, first<- The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:gdata': trim The following object is masked from 'package:grDevices': windows Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: multtest 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: GraphPAC Loading required package: igraph Attaching package: 'igraph' The following object is masked from 'package:Biostrings': union The following object is masked from 'package:XVector': path The following object is masked from 'package:IRanges': union The following object is masked from 'package:S4Vectors': union The following objects are masked from 'package:BiocGenerics': normalize, path, union The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Loading required package: TSP Loading required package: RMallow Loading required package: combinat Attaching package: 'combinat' The following object is masked from 'package:utils': combn Loading required package: SpacePAC Loading required package: data.table Attaching package: 'data.table' The following object is masked from 'package:IRanges': shift The following objects are masked from 'package:S4Vectors': first, second The following objects are masked from 'package:gdata': first, last Warning in file(con, "r") : InternetOpenUrl failed: '' Error: processing vignette 'QuartPAC.Rnw' failed with diagnostics: chunk 1 (label = Example1) Error in file(con, "r") : cannot open the connection --- failed re-building 'QuartPAC.Rnw' SUMMARY: processing the following file failed: 'QuartPAC.Rnw' Error: Vignette re-building failed. Execution halted