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== 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 libapt-pkg-perl libdbd-sqlite3-perl r-base-core r-base-dev
export PERL5LIB=$PERL5LIB:/usr/share/R/share/perl:.
mkdir changelogdb
}}}
 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,CRAN2DEB.pm,patches} .
}}} For later runs only just change to that directory.
 1. Download {{{
../bioc_update.sh --help
# Take some time reading it.
sleep 30 && ../bioc_update.sh Yes!
}}}
 1. Compilation
{{{
   ./cran2deb
}}}

== cran2deb Options ==
{{{
perl cran2deb.pl --help
cran2deb -- Convert R packages from CRAN/BioConductor into Debian packages

Usage:
    cran2deb [options]

Options:
    --help show this help
    --verbose more verbose operation
    --debug even more verbose for debugging purposes
    --dryrun only simulate but don't build
    --binarch arch binary architecture
    --subset regexp regular expression to match package name (set to '')
    --archive path archive mirror
    --repository path repository
    --changelobdbdir path changelogdb directory
    --overwrite build if debian package is found in build directory
    --ignore ignore build errors (for running over night)
    --displayknown display the entries already in the DB
}}}

== Separate Scripts ==

=== findMissingDebs.sh ===

Run within or above the ''builds'' folder. It will give you an output like the following: {{{
Attempted to package:
:-( package affycoretools_1.7.7 not successfully packaged.
:-( package applera_1.5.0 not successfully packaged.
:-( package beadarraysnp_1.1.10 not successfully packaged.
:-( package beadexplorer_1.1.3 not successfully packaged.
:-( package biostrings_2.3.7 not successfully packaged.
:-( package bufferedmatrix_0.1.27 not successfully packaged.
:-( package bufferedmatrixmethods_0.1.1 not successfully packaged.
:-( package cellhts_1.5.8 not successfully packaged.
:-( package isnetwork_1.4.0 not successfully packaged.
:-( package pathrender_1.2.0 not successfully packaged.
:-( package prada_1.11.4 not successfully packaged.
:-( package stam_1.7.0 not successfully packaged.
:-( package tilingarray_1.13.3 not successfully packaged.
:-( package weaver_1.0.1 not successfully packaged.
:-( package widgetinvoke_1.7.0 not successfully packaged.
}}}

Implemented only for ''bioc'': The first argument "sources" will inspect the sources folder for those .tar.gz files that where not even attempted to be built.

=== orig2debSource.sh ===

Given a set of .log files as an argument, this script practically reverses the deletion of the source directory after a failed build.

= 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.
= THIS PAGE IS OBSOLETE =
Go back to AliothPkgBioc.

THIS PAGE IS OBSOLETE

Go back to ?AliothPkgBioc.