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## Auto-converted by kwiki2moinmoin v2005-10-07
== 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 of folders
{{{
   mkdir bioc && cd bioc && ln -s ../cran2deb.pl ../["CRAN2DEB"].pm .
}}}

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.

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= THIS PAGE IS OBSOLETE =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

THIS PAGE IS OBSOLETE

Go back to ?AliothPkgBioc.