Differences between revisions 21 and 22
Revision 21 as of 2006-11-12 00:13:43
Size: 4160
Comment:
Revision 22 as of 2007-02-04 23:49:40
Size: 5265
Comment:
Deletions are marked like this. Additions are marked like this.
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1. check out the tools module via CVS  1. Get some Debian packages {{{
apt-get install libdbd-sqlite3-perl r-base-core r-base-dev
export PERL5LIB=$PERL5LIB:/usr/share/R/share/perl:.
mkdir changelogdb builds
}}}
 1. Checkout the tools module via CVS
Line 17: Line 22:
2. Preparation  1. Preparation
Line 24: Line 29:
3. Mirroring
 * Software{{{
   wget -r --reject css,txt,zip,pdf,html,htm -l 2 -N -nH \
   http://www.bioconductor.org/packages/2.0/bioc/
 1. Download
Well. This was long hampering progress since upstream somehoe
does not open the directory for access and hence inspection of the version number for wget to perform the download, much in contrast to CRAN. Also, there are different repositories for data, experiments and the computational libraries. Upstream provides a script to perform the automated installation, but this is not what we want. The following approach will deny access to hackers' heaven, but, I kind of liked it: {{{
Rversion=2.5
if [ ! -d sources]; then mkdir sources; fi
wget http://www.bioconductor.org/installScripts/$Rversion/biocinstall.R
sed -e 's/install.packages/download.packages/' -e 's/biocinstall/biocdownload/g' -e 's/dependencies=dependencies/destdir="sources"/' < biocinstall.R > biocdownload.R
echo 'biocdownload(group="lite")' >> biocdownload.R
R --no-save < biocdownload.R
Line 29: Line 39:
 * Experiment Data
 * Annotation{{{
   rooturl="http://www.bioconductor.org/packages/2.0/data/annotation/html/"
Line 33: Line 40:
   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
 1. Compilation
Line 60: Line 42:
   ./cran2deb    ./cran2deb bioc
Line 124: Line 106:

= Bits not removed from the Wiki (yet) =
 * 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.

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. Get some Debian packages

    apt-get install libdbd-sqlite3-perl r-base-core r-base-dev
    export PERL5LIB=$PERL5LIB:/usr/share/R/share/perl:.
    mkdir changelogdb builds
  2. Checkout the tools module via CVS
  3. Without account on alioth.debian.org

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

    export CVS_RSH=ssh
    cvs -d :ext:developername@cvs.alioth.debian.org:/cvsroot/pkg-bioc checkout tools 
  5. Preparation
  6. First run ever

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

       cd bioc
  8. Download

Well. This was long hampering progress since upstream somehoe does not open the directory for access and hence inspection of the version number for wget to perform the download, much in contrast to CRAN. Also, there are different repositories for data, experiments and the computational libraries. Upstream provides a script to perform the automated installation, but this is not what we want. The following approach will deny access to hackers' heaven, but, I kind of liked it:

Rversion=2.5
if [ ! -d sources]; then mkdir sources; fi
wget http://www.bioconductor.org/installScripts/$Rversion/biocinstall.R
sed -e 's/install.packages/download.packages/' -e 's/biocinstall/biocdownload/g' -e 's/dependencies=dependencies/destdir="sources"/' < biocinstall.R > biocdownload.R
echo 'biocdownload(group="lite")' >> biocdownload.R 
R --no-save <  biocdownload.R    
  1. Compilation

   ./cran2deb bioc

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 

Bits not removed from the Wiki (yet)

  • 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.