R/biocManifest.R

In switchr: Installing, Managing, and Switching Between Distinct Sets of Installed Packages

##' DEPCRECATED - Create a manifest of Bioc SVN locations
##' @param bioc_vers A version number for a bioc release, or \code{"devel"} to
##' for the current devel trunk
##' @param software_only logical. Should only software packages be
##' included in the manifest? Defaults to TRUE
##' @return A PkgManifest which contains SVN locations for all
##' packages found in the specified bioc repositories, as well
##' as those listed in \code{not_in_repo}
##' @details  In combination with the \code{lazyRepo} function, this
##' manifest can be used to work from a local, working checkout of a
##' set of inter-dependent Bioconductor packages.
##' @seealso \code{\link{lazyRepo}}
##' @export
BiocSVNManifest = function(bioc_vers = "devel", software_only = TRUE) {
    .Deprecated("Bioconductor is no longer based in SVN. Returning empty manifest")
    return(PkgManifest())

    rpackBase = makeBiocSVNURL("", bioc_vers)
    svnres =    system2("svn", args = c("ls", rpackBase,
                                        "--username=readonly --password=readonly"),
                         stdout = TRUE, stderr = TRUE)
    if(!is.null(attr(svnres, "status")))
        stop("svn ls call failed")
    rpkgs = gsub( "/$", "", svnres)
    rpackurls = paste0(rpackBase, rpkgs)
    
    if(software_only) {
        exppkgs = character()
        expurls = character()
    } else {
        experimentBase = makeBiocSVNURL("", bioc_vers, pkgtype="data")
        exppkgs = gsub( "/$", "",
                    system2("svn", args = c("ls", experimentBase,
                                            "--username=readonly --password=readonly"),
                            stdout = TRUE, stderr = TRUE))
        expurls = paste0(experimentBase, exppkgs)
    }
    pkgs = c(rpkgs, exppkgs)
    urls = c(rpackurls, expurls)
    PkgManifest(name = pkgs, url = urls, type = "svn")
    
        
}