biocinstallRepos <- function() { ## Bioconductor CRAN-style repositories. ## The software repo (bioc) _must_ be the first element. repos <- c( "2.5/bioc", "2.5/data/annotation", "2.5/data/experiment", "2.5/extra" ) mirror <- as.character(getOption("BioC_mirror", "http://www.bioconductor.org")) repos <- paste(mirror, "packages", repos, sep="/") c(repos, "http://brainarray.mbni.med.umich.edu/bioc", "http://cran.fhcrc.org") c(repos, ifelse(getOption("repos")=="@CRAN@", "http://cran.fhcrc.org", getOption("repos"))) } biocinstallPkgGroups <- function(groupName="default") { groupName <- match.arg(groupName, c("default", "affy", "graph", "lite", "monograph", "RBioinf", "biocases", "all")) lite_group <- c( "affy", "affydata", "affyPLM", "annaffy", "annotate", "Biobase", "biomaRt", "Biostrings", "DynDoc", "gcrma", "genefilter", "geneplotter", "hgu95av2.db", "limma", "marray", "multtest", "vsn", "xtable", "affyQCReport") if (groupName == "lite") return(lite_group) default_group <- c( lite_group, "globaltest", "makecdfenv", "pamr", "siggenes", "sma", "statmod", "tkWidgets", "widgetTools") if (groupName == "default") return(default_group) affy_group <- c( "affy", "affycomp", "affydata", "affyPLM", "annaffy", "gcrma", "makecdfenv", "marray", "affyQCReport") if (groupName == "affy") return(affy_group) graph_group <- c("graph", "Rgraphviz", "RBGL") if (groupName == "graph") return(graph_group) monograph_group <- c( "affycomp", "affydata", "affypdnn", "affyPLM", "ALL", "ALLMLL", "AmpAffyExample", "annaffy", "AnnBuilder", "annotate", "arrayQuality", "beta7", "Biobase", "bioDist", "Biostrings", "cMAP", "CoCiteStats", "convert", "e1071", "edd", "estrogen", "exactRankTests", "facsDorit", "factDesign", "gbm", "gcrma", "geneplotter", "golubEsets", "GOstats", "gpls", "graph", "hexbin", "hgu133a", "hgu133atagcdf", "hgu133acdf", "hgu133bcdf", "hgu2beta7", "hgu95av2", "hgu95av2cdf", "hgu95av2probe", "hopach", "hsahomology", "hu6800cdf", "hu6800probe", "humanLLMappings", "ipred", "KEGG", "KEGGSOAP", "kidpack", "limma", "locfit", "LogitBoost", "matchprobes", "mclust", "mlbench", "MLInterfaces", "multtest", "pamr", "prada", "PROcess", "ProData", "randomForest", "rat2302", "RbcBook1", "RBGL", "RColorBrewer", "RCurl", "Rgraphviz", "rrcov", "simpleaffy", "sma", "SpikeInSubset", "SSOAP", "statmod", "vsn", "XML", "xtable", "YEAST", "yeastExpData") if (groupName == "monograph") { warning("'arrayMagic' package is no longer available") return(monograph_group) } RBioinf_group <- c( lite_group, graph_group, "RBioinf", "BiocCaseStudies", "XML", "RCurl", "biomaRt", "GEOquery", "KEGG", "KEGGSOAP", "hgu95av2", "hgu95av2probe", "hgu95av2cdf", "human.db0", "BSgenome.Hsapiens.UCSC.hg18") if (groupName == "RBioinf") return(RBioinf_group) biocases_group <- c( lite_group, graph_group, "ALL", "apComplex", "bioDist", "BiocCaseStudies", "biocGraph", "biomaRt", "CCl4", "CLL", "Category", "class", "convert", "GO.db", "GOstats", "GSEABase", "hgu133a.db", "hgu95av2cdf", "hgu95av2probe", "hopach", "KEGG.db", "kohonen", "lattice", "latticeExtra", "MASS", "matchprobes", "MLInterfaces", "org.Hs.eg.db", "ppiStats", "randomForest", "RColorBrewer", "Rintact", "sma", "weaver", "yeastExpData" ) if (groupName == "biocases") return(biocases_group) bioc_url <- biocinstallRepos()[[1]] contriburl <- paste(bioc_url, "src/contrib", sep="/") all_group <- available.packages(contriburl)[, "Package"] names(all_group) <- NULL if (groupName == "all") return(all_group) ## Should never happen stop("unknown groupName ", sQuote(groupName)) } ### biocinstall() version 2.5.11 ### Called by biocLite() when R version 2.10 is detected. ### ### Install Bioconductor packages using CRAN-style repositories. ### Arguments: ### ### pkgs: character vector of Bioconductor packages to install. ### The groupName argument will be ignored if pkgs is specified. ### ### groupName: character matching one of "default", "affy", "graph", "lite", ### "monograph", "all". ### ### repos: the user should not try to pass this argument. It's in the argument list ### of biocinstall() only because we want to raise an error when ### the user tries to pass it. ### ### ...: extra arguments passed to install.packages (see install.packages documentation). biocinstall <- function(pkgs, groupName="default", repos, ...) { ## !!! Always change VERSION when updating this file !!! VERSION <- "2.5.11" # this script version BIOC_VERSION <- "2.5" # this version of Bioconductor thisRVer <- paste(R.Version()[c("major", "minor")], collapse=".") cat("Using R version ", thisRVer, ", ", "biocinstall version ", VERSION, ".\n", sep="") stopifnot(require("utils")) if (missing(pkgs)) pkgs <- biocinstallPkgGroups(groupName) cat("Installing Bioconductor version", BIOC_VERSION, "packages:\n") print(pkgs) cat("Please wait...\n\n") if (!missing(repos)) stop("'repos' argument to the 'biocinstall' function not allowed\n") repos <- biocinstallRepos() type <- list(...)[["type"]] if (is.null(type)) type <- getOption("pkgType") if (type %in% c("mac.binary", "mac.binary.leopard")) { mbniPkgs <- intersect(pkgs, row.names(available.packages( "http://brainarray.mbni.med.umich.edu/bioc/src/contrib"))) if (length(mbniPkgs) > 0) { mbniList <- paste(mbniPkgs, collapse = ", ") warning(paste("MBNI Brain Array packages (", mbniList, ") are not available ", "as Mac binaries. Please use biocLite again with type='source'.", sep="")) } } install.packages(pkgs=pkgs, repos=repos, ...) }