biocinstall.defaultPkgs <- function() { c("affy", "affydata", "affyPLM", "annaffy", "annotate", "Biobase", "Biostrings", "DynDoc", "edd", "gcrma", "genefilter", "geneplotter", "globaltest", "hgu95av2", "limma", "makecdfenv", "marray", "matchprobes", "multtest", "pamr", "ROC", "siggenes", "sma", "statmod", "tkWidgets", "vsn", "widgetTools", "xtable") } biocinstall.affyPkgs <- function() { c("affy", "affycomp", "affydata", "affyPLM", "annaffy", "gcrma", "makecdfenv", "matchprobes", "marray") } biocinstall.graphPkgs <- function() { c("graph", "Rgraphviz", "RBGL") } biocinstall.litePkgs <- function() { c("affy", "affydata", "affyPLM", "annaffy", "annotate", "Biobase", "Biostrings", "DynDoc", "gcrma", "genefilter", "geneplotter", "hgu95av2", "limma", "marray", "matchprobes", "multtest", "ROC", "vsn", "xtable") } biocinstall.monographPkgs <- function() { c("affycomp", "affydata", "affypdnn", "affyPLM", "ALL", "ALLMLL", "AmpAffyExample", "annaffy", "AnnBuilder", "annotate", "arrayMagic", "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", "reposTools", "Rgraphviz", "rrcov", "simpleaffy", "sma", "SpikeInSubset", "SSOAP", "statmod", "vsn", "XML", "xtable", "YEAST", "yeastExpData") } biocinstall.allPkgs <- function() { contriburl = "http://s3.amazonaws.com/bioc-static-website/packages/1.8/bioc/src/contrib" available.packages(contriburl)[, "Package"] } ## biocinstall() version 1.8.5 ## Called by biocLite() when R version 2.3.z 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() just because we wan't to catch the situation when ## the user tries to pass it. ## ## dependencies: passed to install.packages (see install.packages documentation). ## ## type: passed to install.packages (see install.packages documentation). ## ## ...: extra arguments passed to install.packages (see install.packages documentation). biocinstall <- function(pkgs, groupName="default", repos, dependencies=c("Depends", "Imports"), type=getOption("pkgType"), ...) { # !!! Always change version number when updating this file !!! VERSION <- "1.8.5" # R version 2.3.z should have been detected by biocLite() thisRVer <- paste(R.Version()[c("major", "minor")], collapse=".") cat(paste("Running biocinstall version", VERSION, "with R version", thisRVer, "\n")) cat("Your version of R requires version 1.8 of Bioconductor.\n") if (missing(pkgs)) { pkgs <- switch(groupName, "default"=biocinstall.defaultPkgs(), "affy"=biocinstall.affyPkgs(), "graph"=biocinstall.graphPkgs(), "lite"=biocinstall.litePkgs(), "monograph"=biocinstall.monographPkgs(), "all"=biocinstall.allPkgs(), stop("unknown groupName ", sQuote(groupName))) cat("Will install the following packages:\n") print(pkgs) cat("Please wait...\n\n") } if (!missing(repos)) stop("You can't pass a 'repos' argument to the 'biocinstall' function\n") ## CRAN-style Repositories where we'll look for packages repos <- c( "bioc", "data/annotation", "data/experiment", "omegahat", "lindsey" ) repos <- paste("http://s3.amazonaws.com/bioc-static-website/packages/1.8", repos, sep="/") repos <- c(repos, "http://cran.fhcrc.org") install.packages(pkgs=pkgs, repos=repos, dependencies=dependencies, type=type, ...) }