DebianBIOC - Debian Wiki

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