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distrib > Mandriva > 2006.0 > x86_64 > by-pkgid > 33e725ec1aa623b007495df9936953fc > files > 7

R-bioconductor-1.4-3mdk.src.rpm

%define ver	1.4
%define rel	3mdk

# Find a free display (resources generation requires X) and sets XDISPLAY
%define init_xdisplay XDISPLAY=2; while /bin/true; do if [ ! -f /tmp/.X$XDISPLAY-lock ]; then sleep 2s; ( /usr/X11R6/bin/Xvfb -ac :$XDISPLAY >& /dev/null & ); sleep 5s; if [ -f /tmp/.X$XDISPLAY-lock ]; then break; fi; fi; XDISPLAY=$(($XDISPLAY+1)); done

# The virtual X server PID
%define kill_xdisplay kill $(cat /tmp/.X$XDISPLAY-lock)

Summary: A set of R libraries for statistical analysis of genomic data
Name: R-bioconductor
Version: %{ver}
Release: %{rel}
Source0: http://www.bioconductor.org/repository/release%{ver}/package/Source/reposTools_1.4.3.tar.gz
Source1: http://www.bioconductor.org/repository/release%{ver}/package/Source/widgetTools_1.4.2.tar.gz
Source2: http://www.bioconductor.org/repository/release%{ver}/package/Source/DynDoc_1.4.0.tar.gz
Source3: http://www.bioconductor.org/repository/release%{ver}/package/Source/tkWidgets_1.5.10.tar.gz
Source4: http://www.bioconductor.org/repository/release%{ver}/package/Source/Biobase_1.4.15.tar.gz
Source5: http://www.bioconductor.org/repository/release%{ver}/package/Source/Biostrings_1.0.0.tar.gz
Source6: http://www.bioconductor.org/CRANrepository/statmod_1.0.6.tar.gz
Source7: http://www.bioconductor.org/CRANrepository/sma_0.5.14.tar.gz
Source8: http://www.bioconductor.org/repository/release%{ver}/package/Source/limma_1.6.7.tar.gz
Source9: http://www.bioconductor.org/repository/release%{ver}/package/Source/marray_1.5.14.tar.gz
Source10: http://www.bioconductor.org/repository/release%{ver}/package/Source/convert_1.1.7.tar.gz
Source11: http://www.bioconductor.org/repository/release%{ver}/package/Source/ctc_1.2.7.tar.gz
Source12: http://www.bioconductor.org/repository/release%{ver}/package/Source/externalVector_1.0.12.tar.gz
Source13: http://www.bioconductor.org/repository/release%{ver}/package/Source/exprExternal_1.0.0.tar.gz
Source14: http://www.bioconductor.org/repository/release%{ver}/package/Source/Icens_1.0.0.tar.gz
Source15: http://www.bioconductor.org/repository/release%{ver}/package/Source/rhdf5_1.4.0.tar.gz
Source16: http://www.bioconductor.org/repository/release%{ver}/package/Source/daMA_1.0.1.tar.gz
Source17: http://www.bioconductor.org/data/experimental/repos/golubEsets_1.0.tar.gz
Source18: http://www.bioconductor.org/CRANrepository/xtable_1.2-3.tar.gz
Source19: http://www.bioconductor.org/repository/release%{ver}/package/Source/edd_1.4.0.tar.gz
Source20: http://www.bioconductor.org/CRANrepository/XML_0.95-6.tar.gz
Source21: http://www.bioconductor.org/data/metaData/hgu95av2_1.5.1.tar.gz
Source22: http://www.bioconductor.org/repository/release%{ver}/package/Source/genefilter_1.4.0.tar.gz
Source23: http://www.bioconductor.org/repository/release%{ver}/package/Source/annotate_1.4.0.tar.gz
Source24: http://www.bioconductor.org/repository/release%{ver}/package/Source/Ruuid_1.4.2.tar.gz
Source25: http://www.bioconductor.org/CRANrepository/SparseM_0.51.tar.gz
Source26: http://www.bioconductor.org/data/experimental/repos/fibroEset_1.0.tar.gz
Source27: http://www.bioconductor.org/data/metaData/hu6800_1.5.1.tar.gz
Source28: http://www.bioconductor.org/data/metaData/hgu133a_1.5.1.tar.gz
Source29: http://www.bioconductor.org/repository/release%{ver}/package/Source/geneplotter_1.4.0.tar.gz
Source30: http://www.bioconductor.org/repository/release%{ver}/package/Source/ROC_1.0.11.tar.gz
Source31: http://www.bioconductor.org/repository/release%{ver}/package/Source/multtest_1.4.1.tar.gz
Source32: http://www.bioconductor.org/CRANrepository/pamr_1.12.1.tar.gz
Source34: http://www.bioconductor.org/repository/release%{ver}/package/Source/RMAGEML_2.0.8.tar.gz
Source35: http://www.bioconductor.org/repository/release%{ver}/package/Source/siggenes_1.0.6.tar.gz
Source36: http://www.bioconductor.org/repository/release%{ver}/package/Source/globaltest_2.1.6.tar.gz
Source37: http://www.bioconductor.org/repository/release%{ver}/package/Source/affy_1.4.32.tar.gz
Source38: http://www.bioconductor.org/data/cdfenvs/repos/hgu95av2cdf_1.4.3.tar.gz
Source39: http://www.bioconductor.org/data/cdfenvs/repos/hgu133acdf_1.4.3.tar.gz
Source40: http://www.bioconductor.org/repository/release%{ver}/package/Source/affydata_1.4.0.tar.gz
Source41: http://www.bioconductor.org/repository/release%{ver}/package/Source/marrayClasses_1.2.9.tar.gz
Source42: http://www.bioconductor.org/repository/release%{ver}/package/Source/marrayInput_1.1.9.tar.gz
Source43: http://www.bioconductor.org/repository/release%{ver}/package/Source/marrayPlots_1.1.13.tar.gz
Source44: http://www.bioconductor.org/repository/release%{ver}/package/Source/marrayNorm_1.1.11.tar.gz
Source45: http://www.bioconductor.org/repository/release%{ver}/package/Source/vsn_1.4.13.tar.gz
Source46: http://www.bioconductor.org/data/metaData/GO_1.5.1.tar.gz
Source47: http://www.bioconductor.org/data/metaData/KEGG_1.5.1.tar.gz
Source48: http://www.bioconductor.org/repository/release%{ver}/package/Source/annaffy_1.0.7.tar.gz
Source49: http://www.bioconductor.org/repository/release%{ver}/package/Source/affyPLM_1.1.6.tar.gz
Source50: http://www.bioconductor.org/data/probes/Packages/hgu95av2probe_1.0.tar.gz
Source51: http://www.bioconductor.org/data/cdfenvs/repos/hu6800cdf_1.4.3.tar.gz
Source52: http://www.bioconductor.org/data/probes/Packages/hu6800probe_1.0.tar.gz
Source53: http://www.bioconductor.org/repository/release%{ver}/package/Source/matchprobes_1.0.12.tar.gz
Source54: http://www.bioconductor.org/repository/release%{ver}/package/Source/gcrma_1.1.0.tar.gz
Source55: http://www.bioconductor.org/repository/release%{ver}/package/Source/makecdfenv_1.4.7.tar.gz

Source100: http://cran.r-project.org/src/contrib/hdf5_1.5.3.tar.gz

License: GPL
Group: Sciences/Mathematics
URL: http://www.bioconductor.org
BuildRoot: %{_tmppath}/%{name}-%{version}-root
BuildRequires: R-base
BuildRequires: libhdf5-devel
Requires: R-base >= 2.0.0
PreReq: R-base >= 2.0.0

%description
The Bioconductor project produces an open source software framework
that will assist biologists and statisticians working in
bioinformatics, with primary emphasis on inference using DNA
microarrays.

%prep
%setup -c -n R-bioconductor-%{ver} -T

%install
rm -rf %{buildroot}
mkdir -p %{buildroot}/%{_libdir}/R/library

R_LIBS=%{buildroot}%{_libdir}/R/library
export R_LIBS

%{init_xdisplay}
export DISPLAY=:$XDISPLAY

# hdf5
R CMD INSTALL %{SOURCE100} -l %{buildroot}%{_libdir}/R/library

# reposTools
R CMD INSTALL %{SOURCE0} -l %{buildroot}%{_libdir}/R/library

# widgetTools
R CMD INSTALL %{SOURCE1} -l %{buildroot}%{_libdir}/R/library

# DynDoc
R CMD INSTALL %{SOURCE2} -l %{buildroot}%{_libdir}/R/library

# tkWidget
R CMD INSTALL %{SOURCE3} -l %{buildroot}%{_libdir}/R/library

# Biobase

R CMD INSTALL %{SOURCE4} -l %{buildroot}%{_libdir}/R/library

# Biostrings
R CMD INSTALL %{SOURCE5} -l %{buildroot}%{_libdir}/R/library

# statmod
R CMD INSTALL %{SOURCE6} -l %{buildroot}%{_libdir}/R/library

# sma
R CMD INSTALL %{SOURCE7} -l %{buildroot}%{_libdir}/R/library

# limma
R CMD INSTALL %{SOURCE8} -l %{buildroot}%{_libdir}/R/library

# marray
R CMD INSTALL %{SOURCE9} -l %{buildroot}%{_libdir}/R/library

# convert
R CMD INSTALL %{SOURCE10} -l %{buildroot}%{_libdir}/R/library

# ctc
R CMD INSTALL %{SOURCE11} -l %{buildroot}%{_libdir}/R/library

# externalVector
R CMD INSTALL %{SOURCE12} -l %{buildroot}%{_libdir}/R/library

# exprExternal
R CMD INSTALL %{SOURCE13} -l %{buildroot}%{_libdir}/R/library

# Icens
R CMD INSTALL %{SOURCE14} -l %{buildroot}%{_libdir}/R/library

# rhdf5
R CMD INSTALL %{SOURCE15} -l %{buildroot}%{_libdir}/R/library

# daMA
R CMD INSTALL %{SOURCE16} -l %{buildroot}%{_libdir}/R/library

# goluEsets
R CMD INSTALL %{SOURCE17} -l %{buildroot}%{_libdir}/R/library

# xtable
R CMD INSTALL %{SOURCE18} -l %{buildroot}%{_libdir}/R/library

# edd
R CMD INSTALL %{SOURCE19} -l %{buildroot}%{_libdir}/R/library

# XML
R CMD INSTALL %{SOURCE20} -l %{buildroot}%{_libdir}/R/library

# hgu95av2
R CMD INSTALL %{SOURCE21} -l %{buildroot}%{_libdir}/R/library

# genefilter
R CMD INSTALL %{SOURCE22} -l %{buildroot}%{_libdir}/R/library

# annotate
R CMD INSTALL %{SOURCE23} -l %{buildroot}%{_libdir}/R/library

# Ruiid
R CMD INSTALL %{SOURCE24} -l %{buildroot}%{_libdir}/R/library

# SparseM
R CMD INSTALL %{SOURCE25} -l %{buildroot}%{_libdir}/R/library

# FibroEset
R CMD INSTALL %{SOURCE26} -l %{buildroot}%{_libdir}/R/library

# hu6800
R CMD INSTALL %{SOURCE27} -l %{buildroot}%{_libdir}/R/library

# hgu133a
R CMD INSTALL %{SOURCE28} -l %{buildroot}%{_libdir}/R/library

# geneplotter
R CMD INSTALL %{SOURCE29} -l %{buildroot}%{_libdir}/R/library

# ROC
R CMD INSTALL %{SOURCE30} -l %{buildroot}%{_libdir}/R/library

# multtest
R CMD INSTALL %{SOURCE31} -l %{buildroot}%{_libdir}/R/library

# pamr
R CMD INSTALL %{SOURCE32} -l %{buildroot}%{_libdir}/R/library

# SJava
#R CMD INSTALL %{SOURCE33} -l %{buildroot}%{_libdir}/R/library

# RMAGEML
R CMD INSTALL %{SOURCE34} -l %{buildroot}%{_libdir}/R/library

# siggenes
R CMD INSTALL %{SOURCE35} -l %{buildroot}%{_libdir}/R/library

# globaltest
R CMD INSTALL %{SOURCE36} -l %{buildroot}%{_libdir}/R/library

# affy
R CMD INSTALL %{SOURCE37} -l %{buildroot}%{_libdir}/R/library

# hgu95av2cdf
R CMD INSTALL %{SOURCE38} -l %{buildroot}%{_libdir}/R/library

# hgu133acdf
R CMD INSTALL %{SOURCE39} -l %{buildroot}%{_libdir}/R/library

# affydata
R CMD INSTALL %{SOURCE40} -l %{buildroot}%{_libdir}/R/library

# marrayClasses
R CMD INSTALL %{SOURCE41} -l %{buildroot}%{_libdir}/R/library

# marrayInput
R CMD INSTALL %{SOURCE42} -l %{buildroot}%{_libdir}/R/library

# marrayPlots
R CMD INSTALL %{SOURCE43} -l %{buildroot}%{_libdir}/R/library

# marrayNorm
R CMD INSTALL %{SOURCE44} -l %{buildroot}%{_libdir}/R/library

# vsn
R CMD INSTALL %{SOURCE45} -l %{buildroot}%{_libdir}/R/library

# GO
R CMD INSTALL %{SOURCE46} -l %{buildroot}%{_libdir}/R/library

# KEGG
R CMD INSTALL %{SOURCE47} -l %{buildroot}%{_libdir}/R/library

# annaffy
R CMD INSTALL %{SOURCE48} -l %{buildroot}%{_libdir}/R/library

# affyPLM
R CMD INSTALL %{SOURCE49} -l %{buildroot}%{_libdir}/R/library

# hgu95av2probe
R CMD INSTALL %{SOURCE50} -l %{buildroot}%{_libdir}/R/library

# hu6800cdf
R CMD INSTALL %{SOURCE51} -l %{buildroot}%{_libdir}/R/library

# hu6800probe
R CMD INSTALL %{SOURCE52} -l %{buildroot}%{_libdir}/R/library

# matchprobes
R CMD INSTALL %{SOURCE53} -l %{buildroot}%{_libdir}/R/library

# gcrma
R CMD INSTALL %{SOURCE54} -l %{buildroot}%{_libdir}/R/library

# makecdfenv
R CMD INSTALL %{SOURCE55} -l %{buildroot}%{_libdir}/R/library

%{kill_xdisplay}

# this is already included in R-base
rm -f %{buildroot}%{_libdir}/R/library/R.css

%clean
%__rm -rf %{buildroot}

%post 
%{_bindir}/R CMD perl %{_libdir}/R/share/perl/build-help.pl --htmllists > /dev/null 2>&1
%__cat %{_libdir}/R/library/*/CONTENTS > %{_libdir}/R/doc/html/search/index.txt

%postun
%{_bindir}/R CMD perl %{_libdir}/R/share/perl/build-help.pl --htmllists > /dev/null 2>&1
%__cat %{_libdir}/R/library/*/CONTENTS > %{_libdir}/R/doc/html/search/index.txt

%files 
%defattr(-, root, root)
%{_libdir}/R/library/*

%changelog
* Tue Dec 07 2004 Giuseppe Ghibò <ghibo@mandrakesoft.com> 1.4-3mdk
- Rebuilt for 2.0.1.

* Sat Nov 14 2004 Giuseppe Ghibò <ghibo@mandrakesoft.com> 1.4-2mdk
- Rebuilt for R 2.0.
- Updates matchprobes to 1.0.12.

* Sat Oct 02 2004 Giuseppe Ghibò <ghibo@mandrakesoft.com> 1.4-1mdk
- initial release.

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