R/biocinstallRepos.R

In psolaimani/BiocInstaller: Install/Update Bioconductor and CRAN Packages

## TODO: should probably print out a message about how to use mirrors,
## the way sourcing biocLite.R does now.

biocinstallRepos <-
    function(siteRepos=character(), version=biocVersion())
{
    biocVersion <- as.package_version(version)

    old.opts <- options("repos")
    on.exit(options(old.opts))

    ## Starting at some point in R-2.14, Omegahat is included in
    ## the list of available repositories, on windows only, it seems.

    ## on mac and linux:
    
    ## 1: + CRAN
    ## 2: + CRAN (extras)
    ## 3: + BioC software
    ## 4: + BioC annotation
    ## 5: + BioC experiment
    ## 6: + BioC extra
    ## 7:   R-Forge
    ## 8:   rforge.net
    
    ## on windows:
    
    ## 1: + CRAN
    ## 2: + CRAN (extras)
    ## 3:   Omegahat 
    ## 4:   BioC software
    ## 5:   BioC annotation
    ## 6:   BioC experiment
    ## 7:   BioC extra
    ## 8:   R-Forge
    ## 9:   rforge.net
    
    ## So it's probably better not to rely on the numbers.
    
    setRepositories(ind=1:20) # in case more repos are added
    repos <- getOption("repos")

    biocMirror <- getOption("BioC_mirror",
                            sprintf("%s//bioconductor.org", .protocol()))
    biocPaths <- c(BioCsoft="bioc", BioCann="data/annotation",
                    BioCexp="data/experiment", BioCextra="extra")
    biocRepos <- paste(biocMirror, "packages", biocVersion,
                        biocPaths, sep="/")
    repos[names(biocPaths)] <- biocRepos

    keepRepos <- if (.Platform$OS.type %in% "windows") {
        c(names(biocPaths), "CRAN", "CRANextra")
    } else {
        c(names(biocPaths), "CRAN")
    }
    repos <- repos[keepRepos]

    ## This needs to be commented out a few months (3? 4?) after the
    ## next development cycle has started, when we are confident that
    ## no developper is still using an early R devel with a
    ## tools:::.BioC_version_associated_with_R_version still pointing
    ## to the release repository.
    if (!IS_USER)
    {
        ## comment repos here as they become available.
        inactive <- c(
                      ##   "BioCsoft"
                      ## , "BioCextra"
                      ## , "BioCann"
                      ## , "BioCexp"
                      )

        ## No need to touch below.
        tmpRepos <- paste(biocMirror, "packages", DOWNGRADE_VERSION,
                          biocPaths[inactive], sep="/")
        repos[inactive] <- tmpRepos
    }
    
    repos <- subset(repos, !is.na(repos))

    if ("@CRAN@" %in% repos)
        repos["CRAN"] <- sprintf("%s//cran.rstudio.com", .protocol())
    if (includeMBNI &&
        (getOption("pkgType") %in% c("source", "win.binary")))
        repos[["MBNI"]] <- mbniUrl
    
    c(siteRepos=siteRepos, repos)
}