############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data IdeoViz ### ############################################################################## ############################################################################## * checking for file ‘IdeoViz/DESCRIPTION’ ... OK * preparing ‘IdeoViz’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘Vignette.Rnw’ using Sweave Loading required package: IdeoViz Loading required package: Biobase Loading required package: BiocGenerics 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, 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Loading required package: stats4 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: GenomicRanges Loading required package: GenomeInfoDb Loading required package: RColorBrewer Loading required package: rtracklayer Warning in .local(x, ...) : 'track' parameter is deprecated now you go by the 'table' instead Use ucscTables(genome, track) to retrieve the list of tables for a track Error: processing vignette 'Vignette.Rnw' failed with diagnostics: chunk 2 (label = example1) Error in h(simpleError(msg, call)) : error in evaluating the argument 'object' in selecting a method for function 'getTable': Unknown track: cytoBandIdeo --- failed re-building ‘Vignette.Rnw’ SUMMARY: processing the following file failed: ‘Vignette.Rnw’ Error: Vignette re-building failed. Execution halted