Differences between revisions 17 and 18
Revision 17 as of 2006-11-11 22:40:20
Size: 4226
Comment: Describing login as developer.
Revision 18 as of 2006-11-11 22:54:27
Size: 4231
Comment: little rephrasing
Deletions are marked like this. Additions are marked like this.
Line 2: Line 2:
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 [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.
Line 9: Line 10:
 * Without account on alioth.debian.org
{{{
 * Without account on alioth.debian.org{{{
Line 13: Line 13:
 * With account on alioth.debian.org
{{{
 * With account on alioth.debian.org{{{

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. check out the tools module via CVS

  • Without account on alioth.debian.org

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

    export CVS_RSH=ssh
    cvs -d :ext:developername@cvs.alioth.debian.org:/cvsroot/pkg-bioc checkout tools 

2. Preparation

  • First run ever

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

       cd bioc

3. 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.

4. 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