2012/src/image/biocLite.R

In c5sire/GTDMS: Tools for managing and analyzing breeding data of clonal crops

## Mirrors: uncomment the following and change to your favorite CRAN mirror
## if you don't want to use the default (cran.fhcrc.org, Seattle, USA).
## options("repos" = "http://cran.fhcrc.org")

## Mirrors: uncomment the following and change to your favorite Bioconductor
## mirror, if you don't want to use the default (www.bioconductor.org,
## Seattle, USA)
## options("BioC_mirror" = "http://www.bioconductor.org")

local({
			vers <- getRversion()
			biocVers <-
					tryCatch(tools:::.BioC_version_associated_with_R_version,
							error=function(...) numeric_version(0.0))
			if (vers > "2.13" && biocVers > "2.8") {
				if ("biocLite" %in% ls(envir=.GlobalEnv)) {
					message <- paste("You have an outdated biocLite() function.",
							"Run 'rm(biocLite)' and try again.")
					stop(message)
				}
				
				if (!suppressWarnings(require("BiocInstaller", quietly=TRUE))) {
					a <- NULL
					p <- file.path(Sys.getenv("HOME"), ".R", "repositories")
					if (file.exists(p)) {
						a <- tools:::.read_repositories(p)
						if (!"BioCsoft" %in% rownames(a)) 
							a <- NULL
					}
					if (is.null(a)) {
						p <- file.path(R.home("etc"), "repositories")
						a <- tools:::.read_repositories(p)
					}
					if (!"package:utils" %in% search()) {
						url <- "http://bioconductor.org/biocLite.R"
						txt <- sprintf("use 'source(\"%s\")' to update 'BiocInstaller'
										after 'utils' package is attached",
								url)
						message(paste(strwrap(txt), collapse="\n  "))
					} else {
						if (vers == "2.15") {
							a["BioCsoft", "URL"] <- sub(as.character(biocVers), "2.10",
									a["BioCsoft", "URL"])
							biocVers <- numeric_version("2.10")
						}
						
						install.packages("BiocInstaller", repos=a["BioCsoft", "URL"])
						if (!suppressWarnings(require("BiocInstaller",
										quietly=TRUE))) {
							url0 <- "http://www.bioconductor.org/packages"
							url <- sprintf("%s/%s/bioc",
									url0, as.character(biocVers))
							txt0 <- "'biocLite.R' failed to install 'BiocInstaller',
									use 'install.packages(\"%s\", repos=\"%s\")'"
							txt <- sprintf(txt0, "BiocInstaller", url)
							message(paste(strwrap(txt), collapse="\n  "))
						}
					}
				}
			} else {
				source("http://bioconductor.org/getBioC.R")
				biocLite <<-
						function(pkgs, groupName="lite", ...)
				{
					if (missing(pkgs))
						biocinstall(groupName=groupName, ...)
					else
						biocinstall(pkgs=pkgs, groupName=groupName, ...)
				}
			}
		})