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

The following steps are required to prepare all BioConductor packages:

0. check out the tools module via CVS
{{{
cvs -z3 -d:pserver:anonymous@cvs.alioth.debian.org:/cvsroot/pkg-bioc co tools
}}}
1. Preparation
 * First run ever{{{
mkdir bioc && cd bioc && ln -s ../tools/cran2deb.pl ../tools/CRAN2DEB.pm .
}}}
 * Later runs{{{
   cd bioc
}}}
2. Mirroring
 * Tools{{{
   wget -r --reject zip -l 2 -N -nH \
   http://www.bioconductor.org/packages/bioc/devel/src/contrib/html/
}}}
 * Experiment Data
 * Annotation{{{
   for p in \
      http://www.bioconductor.org/packages/data/annotation/stable/src/contrib/html/["humanCHRLOC"].html \
      http://www.bioconductor.org/packages/data/annotation/stable/src/contrib/html/["humanLLMappings"].html \
      http://www.bioconductor.org/packages/data/annotation/stable/src/contrib/html/KEGG.html \
      http://www.bioconductor.org/packages/data/annotation/stable/src/contrib/html/["ratCHRLOC"].html \
      http://www.bioconductor.org/packages/data/annotation/stable/src/contrib/html/["ratLLMappings"].html \
      http://www.bioconductor.org/packages/data/annotation/stable/src/contrib/html/GO.html; \
 do
         wget -r --non-verbose --reject ndex.html,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The tool indicates packages that are outdated and should be removed.

3. Compilation
{{{
   ./cran2deb
}}}

=== Remaining issues ===
 * Compilation of experimental data and annotation packages not yet performed.

 * FTBFS (Fails To Build From Source)
   * stepNorm: cannot represent change to DESCRIPTION: binary file contents changed
   * GeneTraffic: requires SSOAP - is this free? Where?
   * ["aCGH"]: build error - need to investigate
   * prada: preparing package for lazy loading Error in loadNamespace(name) : there is no package called 'prada'
   * rfcdmin: mysterious build error
   * ["RdbiPgSQL"]: needs environment variable for postgresql
   * ["iSPlot"]: dependency to ["RGtk"] (maybe I should try this one again)
   * twilight: cannot represent change to README: binary file contents changed
   * KEGGSOAP: SSOAP (>= 0.2), ["RCurl"] (>= 0.4)
   * gpls: cannot represent change to NAMESPACE: binary file contents changed, also: Error in parse(file, n, text, prompt) : syntax error on line 10

 * Needs metadata which is not yet available
   * annaffy
   * webbioc: needs annaffy which in turn needs metadata
   * ontoTools: needs Metadata
   * ecolitk
   * edd: needs golubEsets
   * goTools: needs meta data
   * geneplotter: needs metadata
   * makePlatformDesign: why didn't I take better notes, I forgot about this one


====== 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
}}}
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