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
Software
wget -r --reject css,txt,zip,pdf,html,htm -l 2 -N -nH \ http://www.bioconductor.org/packages/2.0/bioc/
- Experiment Data
Annotation
rooturl="http://www.bioconductor.org/packages/2.0/data/annotation/html/" for p in \ ${rooturl}["humanCHRLOC"].html \ ${rooturl}["humanLLMappings"].html \ ${rooturl}["ratCHRLOC"].html \ ${rooturl}["ratLLMappings"].html \ ${rooturl}["mouseCHRLOC"].html \ ${rooturl}["mouseLLMappings"].html \ ${rooturl}KEGG.html \ ${rooturl}KEGGdb.html \ ${rooturl}["ratCHRLOC"].html \ ${rooturl}["ratLLMappings"].html \ ${rooturl}GO.html \ ${rooturl}GOdb.html \ ${rooturl}PFAM.html \ ; \ do wget -r --reject css,txt,pdf,html,htm,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The tool indicates packages that are outdated and should be removed.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