OOMPAinstallRepos <- function()
{
    ## OOMPA CRAN-style repositories.
    ## The software repo (OOMPA) _must_ be the first element.
    repos <- c(
        "2.13"
    )
    setRepositories(graphics=FALSE, ind=c(1,4))
    myRepos <- c(getOption("repos"), 
                 OOMPA=paste("http://bioinformatics.mdanderson.org/OOMPA", repos, sep="/"))
    myRepos[length(myRepos)]
}

OOMPAinstallPkgGroups <- function(groupName="default")
{
    groupName <- match.arg(groupName,
                           c("default", "lite", "genalg",
                             "prediction", "supercurve", "all",
                             "arraycube"))

    supercurve.group <- c("tclish", "SuperCurve",
                          "SuperCurveGUI", "SlideDesignerGUI")
                          
    if (groupName == "supercurve")
      return(supercurve.group)

    lite.group <- c("oompaBase", "PreProcess",
                    "ClassDiscovery", "ClassComparison")
    if (groupName == "lite")
      return(lite.group)

    genalg.group <- c(lite.group, "GenAlg")
    if (groupName == "genalg")
      return(genalg.group)

    prediction.group <- c(genalg.group, "TailRank",
                          "CrossVal", "ClassPrediction")
    if (groupName == "prediction")
      return(prediction.group)
    
    default.group <- c(prediction.group, supercurve.group,
                       "TailRank")
    if (groupName == "default")
      return(default.group)

    arraycube.group <- c("oompaBase", "PreProcess", "ArrayCube", "MINiML")
    if (groupName == "arraycube")
      return(arraycube.group)
    
    OOMPA.url <- OOMPAinstallRepos()[[1]]
    contriburl <- paste(OOMPA.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))
}


### OOMPAinstall() version 2.13.0
### Called by OOMPALite() when R version 2.13 is detected.
###
### Install OOMPA packages using CRAN-style repositories.
### Arguments:
###
###   pkgs: character vector of OOMPAonductor 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 OOMPAinstall() only because we want to raise an error 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).

oompainstall <- function(pkgs, groupName="default", repos,
                        dependencies=c("Depends", "Imports"), type=getOption("pkgType"), ...)
{
    ## !!! Always change version number when updating this file !!!
    VERSION <- "2.13.0"
    ## R version 2.13 should have been detected by OOMPALite()
    thisRVer <- paste(R.Version()[c("major", "minor")], collapse=".")
    cat(paste("Running OOMPAinstall version", VERSION, "with R version", thisRVer, "\n"))

    stopifnot(require("utils"))
    cat("Your version of R requires version 2.13 of OOMPA.\n")
    
    if (missing(pkgs)) {
        pkgs <- OOMPAinstallPkgGroups(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 'OOMPAinstall' function\n")

    repos <- OOMPAinstallRepos()

    install.packages(pkgs=pkgs, repos=repos, dependencies=dependencies, type=type, ...)
}