############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r ArrayTools -R && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ArrayTools ### ############################################################################## ############################################################################## * checking for file 'ArrayTools/DESCRIPTION' ... OK * preparing 'ArrayTools': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'ArrayTools.Rnw' using Sweave Loading required package: affy 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 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: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Warning: Package 'ArrayTools' is deprecated and will be removed from Bioconductor version 3.14 Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: org.Hs.eg.db Loading required package: annaffy Loading required package: BiocManager Loading required package: GO.db Error: processing vignette 'ArrayTools.Rnw' failed with diagnostics: chunk 3 Error in h(simpleError(msg, call)) : error in evaluating the argument 'object' in selecting a method for function 'getText': could not find function "aafUniGene" --- failed re-building 'ArrayTools.Rnw' SUMMARY: processing the following file failed: 'ArrayTools.Rnw' Error: Vignette re-building failed. Execution halted