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

The general idea is that upstream's (the BioConductor developers's) install scripts are not aware of the respective Linux distribution and do now know how to install those libraries external to CRAN that are required for the compilation. Some other bits require manual intervention, i.e. for the integration with web servers.

The following steps are required to prepare all BioConductor packages:

 1. Prepare local Debian installation: {{{
apt-get install libdbd-sqlite3-perl r-base-core r-base-dev
export PERL5LIB=$PERL5LIB:/usr/share/R/share/perl:.
mkdir changelogdb builds
}}}
 1. Checkout the pkg-bioc's ''tools'' module via CVS, either
 * anonymously without account on alioth.debian.org{{{
cvs -z3 -d:pserver:anonymous@cvs.alioth.debian.org:/cvsroot/pkg-bioc co tools
}}}
 * or (preferred) with one's on alioth.debian.org{{{
export CVS_RSH=ssh
cvs -d :ext:developername@cvs.alioth.debian.org:/cvsroot/pkg-bioc checkout tools
}}} Only this second route allows the contribution to the project.
 1. Preparations for the packaging script:
 * for first run{{{
mkdir bioc && cd bioc && ln -s ../tools/{cran2deb.pl,CRANDEB.pl,patches) .
}}}
 * Later runs{{{
   cd bioc
}}}
 1. Download
Well. This was long hampering progress since upstream somehow
does not open the directory for accession and hence inspection of the version number of the packages. This would be required for wget to perform the download, much in contrast to CRAN. Also, there are different repositories for data, experiments and the computational libraries. Upstream provides a script to perform the automated installation. The following approach will deny access to hackers' heaven, but, I kind of liked it: {{{
Rversion=`R --version | head -1 |cut -f3 -d\ | cut -f1,2 -d.`
if [ -z "\$Rversion" ]; then
   Rversion=2.4
fi
if [ ! -d sources ]; then mkdir sources; fi
wget http://www.bioconductor.org/installScripts/$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
}}}

== cran2deb Options ==



== Separate Scripts ==

Debian BioConductor archive

The [http://alioth.debian.org/projects/pkg-bioc/ Alioth pkg-bioc] is preparing a repository for Debian packages for the ?BioConductor collection of R libraries.

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

The general idea is that upstream's (the ?BioConductor developers's) install scripts are not aware of the respective Linux distribution and do now know how to install those libraries external to CRAN that are required for the compilation. Some other bits require manual intervention, i.e. for the integration with web servers.

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

  1. Prepare local Debian installation:

    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 pkg-bioc's tools module via CVS, either

  3. anonymously without account on alioth.debian.org

    cvs -z3 -d:pserver:anonymous@cvs.alioth.debian.org:/cvsroot/pkg-bioc co tools
  4. or (preferred) with one's on alioth.debian.org

    export CVS_RSH=ssh
    cvs -d :ext:developername@cvs.alioth.debian.org:/cvsroot/pkg-bioc checkout tools
    Only this second route allows the contribution to the project.
  5. Preparations for the packaging script:
  6. for first run

    mkdir bioc && cd bioc && ln -s ../tools/{cran2deb.pl,CRANDEB.pl,patches) .
  7. Later runs

       cd bioc
  8. Download

Well. This was long hampering progress since upstream somehow does not open the directory for accession and hence inspection of the version number of the packages. This would be required 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. The following approach will deny access to hackers' heaven, but, I kind of liked it:

Rversion=`R --version | head -1 |cut -f3 -d\ | cut -f1,2 -d.`
if [ -z "\$Rversion" ]; then
   Rversion=2.4
fi
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

cran2deb Options

Separate Scripts

Bits not removed from the Wiki (yet)

  • Software

       wget -r --reject css,txt,zip,pdf,html,htm -l 2 -N -nH \
       http://www.bioconductor.org/packages/2.0/bioc/
  • Experiment Data
  • Annotation

       rooturl="http://www.bioconductor.org/packages/2.0/data/annotation/html/"
    
       for p in \
         ${rooturl}["humanCHRLOC"].html \
         ${rooturl}["humanLLMappings"].html \
         ${rooturl}["ratCHRLOC"].html \
         ${rooturl}["ratLLMappings"].html \
         ${rooturl}["mouseCHRLOC"].html \
         ${rooturl}["mouseLLMappings"].html \
         ${rooturl}KEGG.html \
         ${rooturl}KEGGdb.html \
         ${rooturl}["ratCHRLOC"].html \
         ${rooturl}["ratLLMappings"].html \
         ${rooturl}GO.html \
         ${rooturl}GOdb.html \
         ${rooturl}PFAM.html \
     ; \
     do
             wget -r --reject css,txt,pdf,html,htm,zip -l 1 -N -nH $p
     done

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

  • For later runs only:

        (cd packages/bioc/devel/src/contrib/Source/ && deldoubles.pl)

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