Debian BioConductor archive

The [http://alioth.debian.org/projects/pkg-bioc/ Alioth pkg-bioc] is working on a reporitory for Debian packages of the R libraries at ?BioConductor (http://www.bioconductor.org). More information is found on the Wiki page to ?AliothPkgBioc.

The following steps are required to prepare all ?BioConductor packages:

  1. Get some Debian packages

    apt-get install libdbd-sqlite3-perl r-base-core r-base-dev
    export PERL5LIB=$PERL5LIB:/usr/share/R/share/perl:.
    mkdir changelogdb builds
  2. Checkout the tools module via CVS
  3. Without account on alioth.debian.org

    cvs -z3 -d:pserver:anonymous@cvs.alioth.debian.org:/cvsroot/pkg-bioc co tools
  4. With account on alioth.debian.org

    export CVS_RSH=ssh
    cvs -d :ext:developername@cvs.alioth.debian.org:/cvsroot/pkg-bioc checkout tools 
  5. Preparation
  6. First run ever

    mkdir bioc && cd bioc && ln -s ../tools/cran2deb.pl ../tools/CRAN2DEB.pm .
  7. Later runs

       cd bioc
  8. Download

Well. This was long hampering progress since upstream somehoe does not open the directory for access and hence inspection of the version number for wget to perform the download, much in contrast to CRAN. Also, there are different repositories for data, experiments and the computational libraries. Upstream provides a script to perform the automated installation, but this is not what we want. The following approach will deny access to hackers' heaven, but, I kind of liked it:

Rversion=2.5
if [ ! -d sources ]; then mkdir sources; fi
wget http://www.bioconductor.org/installScripts/$Rversion/biocinstall.R
sed -e 's/install.packages/download.packages/' -e 's/biocinstall/biocdownload/g' -e 's/dependencies=dependencies/destdir="sources"/' < biocinstall.R > biocdownload.R
echo 'biocdownload(group="lite")' >> biocdownload.R 
R --no-save <  biocdownload.R    
  1. Compilation

   ./cran2deb bioc

Remaining issues

Currently outdated by newer versions

   AnnBuilder_1.6.2.tar.gz
   annotate_1.6.0.tar.gz
   arrayQuality_1.1.0.tar.gz
   Biobase_1.6.0.tar.gz
   biomaRt_1.1.0.tar.gz
   ctc_1.3.0.tar.gz
   gcrma_1.2.0.tar.gz
   genefilter_1.7.0.tar.gz
   geneplotter_1.7.0.tar.gz
   GeneTS_2.5.0.tar.gz
   globaltest_3.1.0.tar.gz
   graph_1.6.1.tar.gz
   GraphAT_1.1.0.tar.gz
   hopach_1.2.0.tar.gz
   hypergraph_1.1.0.tar.gz
   ideogram_1.1.0.tar.gz
   limma_1.10.0.tar.gz
   maDB_1.1.1.tar.gz
   makecdfenv_1.6.0.tar.gz
   makePlatformDesign_0.0.1.tar.gz
   MLInterfaces_1.1.0.tar.gz
   multtest_1.7.0.tar.gz
   oligo_0.0.3.tar.gz
   prada_1.4.0.tar.gz
   Resourcerer_1.2.1.tar.gz
   Rgraphviz_1.6.0.tar.gz
   Ruuid_1.6.0.tar.gz
   SBMLR_1.21.tar.gz
   siggenes_1.3.0.tar.gz
   simpleaffy_2.1.0.tar.gz
   tkWidgets_1.6.0.tar.gz
   vsn_1.7.1.tar.gz
   xcms_1.1.0.tar.gz 

Bits not removed from the Wiki (yet)

Any suggestion on how to improve the download of a selected number of packages from the annotation packages are welcome.

The tool indicates packages that are outdated and should be removed.