############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data AffyExpress ### ############################################################################## ############################################################################## * checking for file ‘AffyExpress/DESCRIPTION’ ... OK * preparing ‘AffyExpress’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘AffyExpress.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")'. Loading required package: limma Attaching package: ‘limma’ The following object is masked from ‘package:BiocGenerics’: plotMA Warning: Package 'AffyExpress' is deprecated and will be removed from Bioconductor version 3.14 Attaching package: ‘AffyExpress’ The following object is masked from ‘package:BiocGenerics’: Filter The following object is masked from ‘package:base’: Filter Loading required package: R2HTML Loading required package: affyPLM Loading required package: gcrma Loading required package: preprocessCore Loading required package: simpleaffy Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘simpleaffy’ Error: processing vignette 'AffyExpress.Rnw' failed with diagnostics: chunk 2 Error in setQCEnvironment(genome) : could not find function "setQCEnvironment" --- failed re-building ‘AffyExpress.Rnw’ SUMMARY: processing the following file failed: ‘AffyExpress.Rnw’ Error: Vignette re-building failed. Execution halted