%load_ext rmagic
%R source("http://bioconductor.org/biocLite.R")
%R biocLite(c("pkgDepTools", "Biobase", 'Rgraphviz', "BiocInstaller"))
Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help A newer version of Bioconductor is available after installing a new version of R, ?BiocUpgrade for help
BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2. Installing package(s) 'pkgDepTools' 'Biobase' 'Rgraphviz' 'BiocInstaller' versuche URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/pkgDepTools_1.28.0.tar.gz' Content type 'application/x-gzip' length 165306 bytes (161 Kb) URL geöffnet ================================================== downloaded 161 Kb versuche URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/Biobase_2.22.0.tar.gz' Content type 'application/x-gzip' length 1848944 bytes (1.8 Mb) URL geöffnet ================================================== downloaded 1.8 Mb versuche URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/Rgraphviz_2.6.0.tar.gz' Content type 'application/x-gzip' length 7451849 bytes (7.1 Mb) URL geöffnet ================================================== downloaded 7.1 Mb versuche URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/BiocInstaller_1.12.1.tar.gz' Content type 'application/x-gzip' length 13520 bytes (13 Kb) URL geöffnet ================================================== downloaded 13 Kb The downloaded source packages are in ‘/tmp/Rtmp9nbasC/downloaded_packages’
%%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")
[1] "methods" "graphics" "stats" "parallel" [5] "BiocGenerics" "utils" "stats4" "IRanges" [9] "XVector" "GenomicRanges" "Rcpp" "RcppArmadillo" [13] "grid" "grDevices" "lattice" "locfit" [17] "Biobase" "DBI" "RSQLite" "AnnotationDbi" [21] "xtable" "XML" "annotate" "splines" [25] "survival" "genefilter" "RColorBrewer" "DESeq2" [1] "NA/NA_NA.tar.gz" [2] "NA/NA_NA.tar.gz" [3] "NA/NA_NA.tar.gz" [4] "NA/NA_NA.tar.gz" [5] "http://bioconductor.org/packages/2.13/bioc/src/contrib/BiocGenerics_0.8.0.tar.gz" [6] "NA/NA_NA.tar.gz" [7] "NA/NA_NA.tar.gz" [8] "http://bioconductor.org/packages/2.13/bioc/src/contrib/IRanges_1.20.7.tar.gz" [9] "http://bioconductor.org/packages/2.13/bioc/src/contrib/XVector_0.2.0.tar.gz" [10] "http://bioconductor.org/packages/2.13/bioc/src/contrib/GenomicRanges_1.14.4.tar.gz" [11] "http://cran.fhcrc.org/src/contrib/Rcpp_0.11.3.tar.gz" [12] "http://cran.fhcrc.org/src/contrib/RcppArmadillo_0.4.500.0.tar.gz" [13] "NA/NA_NA.tar.gz" [14] "NA/NA_NA.tar.gz" [15] "http://cran.fhcrc.org/src/contrib/lattice_0.20-29.tar.gz" [16] "http://cran.fhcrc.org/src/contrib/locfit_1.5-9.1.tar.gz" [17] "http://bioconductor.org/packages/2.13/bioc/src/contrib/Biobase_2.22.0.tar.gz" [18] "http://cran.fhcrc.org/src/contrib/DBI_0.3.1.tar.gz" [19] "http://cran.fhcrc.org/src/contrib/RSQLite_1.0.0.tar.gz" [20] "http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi_1.24.0.tar.gz" [21] "http://cran.fhcrc.org/src/contrib/xtable_1.7-4.tar.gz" [22] "http://cran.fhcrc.org/src/contrib/XML_3.98-1.1.tar.gz" [23] "http://bioconductor.org/packages/2.13/bioc/src/contrib/annotate_1.40.1.tar.gz" [24] "NA/NA_NA.tar.gz" [25] "http://cran.fhcrc.org/src/contrib/survival_2.37-7.tar.gz" [26] "http://bioconductor.org/packages/2.13/bioc/src/contrib/genefilter_1.44.0.tar.gz" [27] "http://cran.fhcrc.org/src/contrib/RColorBrewer_1.0-5.tar.gz" [28] "http://bioconductor.org/packages/2.13/bioc/src/contrib/DESeq2_1.2.10.tar.gz"