biocinstall <- function(pkgs, lib, develOK=FALSE, groupName="default", ...) { ## Install Bioconductor packages using CRAN-style repositories ## ## pkgs: character vector of Bioconductor packages to install. ## The groupName argument will be ignored if pkgs is specified. ## ## lib: character vector giving the library directories where to ## install the packages. Recycled as needed. ## ## ## groupName: character matching one of "affy", "default", ## "graph", "all" ## ## ...: extra arguments passed to install.packages. Of particular interest ## may be the dependencies argument. This script defaults to TRUE for ## R 2.0.x and to "Depends" for R 2.1.x. For R 2.1.x, you can set ## dependencies=c("Depends", "Suggests", "Imports"). Also, destdir ## can be useful as it is used to specify the location to which ## downloaded packages should be stored for R >= 2.1.0 users. For R ## 2.0.x users, destdir is yhe installation directory and if no directory is provided, ## getBioC() will default to using your standard library path. ## ## develOK: Deprecated. To receive developmental software and packages, ## running the development version of R should be practiced. ## !!! Always change version number when updating this file !!! VERSION <- "1.3" #if (develOK) { # stop("develOK has been deprecated. If you would like to use this script for installing developmental packages, you must install the devel version of R.") #} stopifnot(require("utils")) ## Verify we're running a recent enough version of R requiredRVer <- "2.1.0" develVer <- "2.2.0" thisRVer <- paste(R.Version()[c("major", "minor")], collapse=".") if (compareVersion(thisRVer, requiredRVer) < 0) { stop(paste("\nYou are currently running R version ", thisRVer, ", however R version ", requiredRVer, " is required.",sep="")) } if (compareVersion(thisRVer, develVer) >= 0) RDEVEL <- TRUE else RDEVEL <- FALSE cat(paste("\nRunning biocinstall version", VERSION," with R version ", thisRVer, "\n")) biocRepRoot = "http://www.bioconductor.org/packages/bioc" if (!missing(pkgs)) { if (is.null(pkgs) || length(pkgs) == 0) stop("pkgs was set to ", sQuote(pkgs), ". I was expecting a non-empty character vector.") pkgsToInstall <- pkgs } else { ## pkgs missing affyPkgs <- c("affy", "affycomp", "affydata", "affyPLM", "annaffy", "gcrma", "makecdfenv", "matchprobes", "marray") graphPkgs <- c("graph", "Rgraphviz", "RBGL") defaultPkgs <- c("affy", "affydata", "affyPLM", "annaffy", "annotate", "Biobase", "Biostrings", "DynDoc", "edd", "gcrma", "genefilter", "geneplotter", "globaltest", "hgu95av2", "limma", "makecdfenv", "marray", "matchprobes", "multtest", "pamr", "reposTools", "ROC", "siggenes", "sma", "statmod", "tkWidgets", "vsn", "widgetTools", "xtable") litePkgs <- c("affy", "affydata", "affyPLM", "annaffy", "annotate", "Biobase", "Biostrings", "DynDoc", "gcrma", "genefilter", "geneplotter", "hgu95av2", "limma", "marray", "matchprobes", "multtest", "reposTools", "ROC", "vsn", "xtable") if (RDEVEL) biocRep = paste(biocRepRoot, "devel", sep="/") else biocRep = paste(biocRepRoot, "stable", sep="/") # XXX: FIXME!!!!!!!!!!!!!!!!!!!!! allPkgs = CRAN.packages(CRAN=biocRep)[, "Package"] pkgsToInstall <- switch(groupName, "affy"=affyPkgs, "graph"=graphPkgs, "default"=defaultPkgs, "lite"=litePkgs, "all"=allPkgs, stop("unknown groupName ", sQuote(groupName))) } if (missing(lib)) { lib <- .libPaths()[1] } args <- list(...) nms <- names(args) if (! "dependencies" %in% nms) args[["dependencies"]] <- c("Depends", "Imports") ## CRAN-style Repositories where we'll look for packages reposList = c( "http://www.bioconductor.org/packages/bioc/1.6", "http://www.bioconductor.org/packages/data/annotation/1.6", "http://www.bioconductor.org/packages/data/experiment/1.6", "http://www.bioconductor.org/packages/omegahat/1.6", "http://www.bioconductor.org/packages/lindsey/1.6", "http://cran.fhcrc.org") args <- c(list(pkgs=pkgsToInstall, repos=reposList, lib=lib), args) do.call("install.packages", args) }