##' 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")
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.