%load_ext rmagic

%R source("http://bioconductor.org/biocLite.R")
%R biocLite(c("pkgDepTools", "Biobase", 'Rgraphviz', "BiocInstaller"))

%%R 
library("pkgDepTools")
library("Biobase")
library("Rgraphviz")
library("BiocInstaller")

%%R
dependencies <- makeDepGraph(biocinstallRepos(), type="source", keep.builtin=TRUE, dosize=FALSE)
contrib_url <- contrib.url(biocinstallRepos(), type = "source")
available_packages <- available.packages( contrib_url )
package_names <- as.vector( available_packages[,"Package"] )
package_versions <- as.vector( available_packages[,"Version"] )
package_urls <- as.vector(available_packages[,"Repository"])

%%R

getPackageDependencies <- function( package )
{
    packages <- getInstallOrder( package, dependencies, needed.only=FALSE )$packages

    graph <- c(package, names(acc(dependencies, package)[[1]]))
    plot( subGraph(graph, dependencies) )
    print(packages)
    intersect <- match(packages, available_packages )
    intersect <- intersect[ !is.na(intersect) ]
    
    paste( package_urls[intersect], paste(paste( package_names[intersect], package_versions[intersect], sep="_"), "tar.gz", sep="."), sep="/" )
}



%%R
getPackageDependencies("DESeq2")