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Debian BioConductor archive

The {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:

1. Preparation

  • First run ever

       mkdir bioc && cd bioc && ln -s ../cran2deb.pl ../["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The tool indicates packages that are outdated and should be removed.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

}}}