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Add R-ArrayExpressHTS spec and dependencies
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‎R-AnnotationDbi.spec

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%global packname AnnotationDbi
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%global Rvers 2.11.0
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Name: R-%{packname}
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Version: 1.14.1
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Release: 1%{dist}
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Summary: Annotation Database Interface
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Group: Applications/Engineering
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License: Artistic 2.0
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URL: http://bioconductor.org/packages/release/bioc/html/%{packname}.html
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Source0: http://bioconductor.org/packages/release/bioc/src/contrib/%{packname}_%{version}.tar.gz
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BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
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BuildArch: noarch
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# The suggested requirement are not added here based on:
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# - the amount
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# - they are mostly database (content)
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# - circular dependancies (such as with hgu95av2)
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Requires: R-core >= %{Rvers} R-methods R-utils
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Requires: R-Biobase R-DBI R-RSQLite
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BuildRequires: R-devel >= %{Rvers} tex(latex) R-methods
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BuildRequires: R-utils R-Biobase R-DBI R-RSQLite
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%description
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Provides user interface and database connection code for annotation
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data packages using SQLite data storage.
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%prep
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%setup -q -c -n %{packname}
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%build
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%install
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rm -rf %{buildroot}
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# noarch -> Architecture independent package
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mkdir -p %{buildroot}%{_datadir}/R/library
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R CMD INSTALL %{packname} -l %{buildroot}%{_datadir}/R/library
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# Clean up in advance of check
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test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
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rm -rf %{buildroot}%{_datadir}/R/library/R.css
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rm -f %{buildroot}%{_datadir}/R/library/AnnotationDbi/ProbePkg-template/data/.dummy.txt
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%check
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# Not performed, the list of metadata asked is too long and not mandatory
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#%{_bindir}/R CMD check %{packname}
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%clean
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rm -rf %{buildroot}
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%files
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%defattr(-, root, root, -)
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%dir %{_datadir}/R/library/%{packname}
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%doc %{_datadir}/R/library/%{packname}/html
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%doc %{_datadir}/R/library/%{packname}/DESCRIPTION
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%doc %{_datadir}/R/library/%{packname}/doc
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%doc %{_datadir}/R/library/%{packname}/NEWS
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%doc %{_datadir}/R/library/%{packname}/TODO
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%{_datadir}/R/library/%{packname}/INDEX
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%{_datadir}/R/library/%{packname}/NAMESPACE
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%{_datadir}/R/library/%{packname}/Meta
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%{_datadir}/R/library/%{packname}/R
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%{_datadir}/R/library/%{packname}/help
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%{_datadir}/R/library/%{packname}/AnnDbPkg-templates
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%{_datadir}/R/library/%{packname}/ProbePkg-template
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%{_datadir}/R/library/%{packname}/DBschemas
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%{_datadir}/R/library/%{packname}/extdata
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%{_datadir}/R/library/%{packname}/NOTES-Herve
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%changelog
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* Wed Apr 20 2011 Adam Huffman <[email protected]> - 1.14.1-1%{dist}
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- build new version needed by ArrayExpressHTS etc.
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* Mon Feb 07 2011 Fedora Release Engineering <[email protected]> - 1.12.0-2
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild
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* Tue Oct 26 2010 pingou <[email protected]> 1.12.0-1
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- Update to version 1.12.0
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* Sat Sep 11 2010 pingou <[email protected]> 1.10.2-1
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- Update to version 1.10.2
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* Tue May 11 2010 pingou <[email protected]> 1.10.1-1
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- Update to version 1.10.1
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- Fix url to a more stable form
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- Fix R for latex
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- Remove R post/postun
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* Sat Mar 27 2010 pingou <[email protected]> 1.8.2-1
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- Update to 1.8.2
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* Sat Nov 21 2009 pingou <[email protected]> 1.8.1-1
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- Update to 1.8.1
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- Remove the %%post and %%postun
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- Adapt %%files to the new R
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* Sat Aug 01 2009 pingou <[email protected]> 1.6.1-1
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- Update to 1.6.1
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* Wed May 06 2009 pingou <[email protected]> 1.6.0-1
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- initial package for Fedora

‎R-ArrayExpress.spec

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%global packname ArrayExpress
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%global rlibdir %{_datadir}/R/library
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Name: R-%{packname}
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Version: 1.12.0
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Release: 1%{?dist}
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Summary: Access the arrayexpress microarray database at ebi and b
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Group: Applications/Engineering
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License: Artistic-2.0
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URL: http://bioconductor.org/packages/release/bioc/html/ArrayExpress.html
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Source0: http://bioconductor.org/packages/release/bioc/src/contrib/%{packname}_%{version}.tar.gz
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BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
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BuildArch: noarch
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Requires: R-core
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Requires: R >= 2.9.0 R-Biobase >= 2.4.0
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BuildRequires: R-devel tex(latex) R >= 2.9.0 R-Biobase >= 2.4.0 R-XML R-affy R-limma
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%description
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Access the ArrayExpress Repository at EBI and build Bioconductor data
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structures: ExpressionSet, AffyBatch, NChannelSet
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%prep
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%setup -q -c -n %{packname}
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%build
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%install
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rm -rf %{buildroot}
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mkdir -p %{buildroot}%{rlibdir}
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%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname}
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test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
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rm -f %{buildroot}%{rlibdir}/R.css
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%check
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%{_bindir}/R CMD check %{packname}
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%clean
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rm -rf %{buildroot}
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%files
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%defattr(-, root, root, -)
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%dir %{rlibdir}/%{packname}
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%doc %{rlibdir}/%{packname}/doc
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%doc %{rlibdir}/%{packname}/html
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%doc %{rlibdir}/%{packname}/DESCRIPTION
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%doc %{rlibdir}/%{packname}/CITATION
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%{rlibdir}/%{packname}/INDEX
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%{rlibdir}/%{packname}/NAMESPACE
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%{rlibdir}/%{packname}/Meta
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%{rlibdir}/%{packname}/R
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%{rlibdir}/%{packname}/help
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%changelog
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* Wed Apr 20 2011 Adam Huffman <[email protected]> 1.12.0-1
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- initial package for Fedora

‎R-ArrayExpressHTS.spec

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%global packname ArrayExpressHTS
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%global rlibdir %{_libdir}/R/library
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Name: R-%{packname}
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Version: 1.0
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Release: 1%{?dist}
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Summary: Arrayexpress high throughput sequencing package
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Group: Applications/Engineering
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License: Artistic License 2.0
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URL: http://www.ebi.ac.uk/Tools/rwiki/
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Source0: http://www.ebi.ac.uk/Tools/rcloud/downloads/ArrayExpressHTS_1.0.tar.gz
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BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
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Requires: R-svMisc R-sampling R-xtable R-DESeq R-ArrayExpress R-RColorBrewer R-biomaRt
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BuildRequires: R-devel tex(latex) R-svMisc R-sampling R-xtable R-DESeq R-ArrayExpress R-RColorBrewer R-biomaRt
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%description
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RNA Sequencing Processing Pipeline and Analysis
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%prep
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%setup -q -c -n %{packname}
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%build
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%install
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rm -rf %{buildroot}
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mkdir -p %{buildroot}%{rlibdir}
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%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname}
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test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
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rm -f %{buildroot}%{rlibdir}/R.css
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%check
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%{_bindir}/R CMD check %{packname}
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%clean
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rm -rf %{buildroot}
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%files
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%defattr(-, root, root, -)
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%dir %{rlibdir}/%{packname}
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%doc %{rlibdir}/%{packname}/doc
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%doc %{rlibdir}/%{packname}/html
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%doc %{rlibdir}/%{packname}/DESCRIPTION
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%doc %{rlibdir}/%{packname}/NEWS
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%{rlibdir}/%{packname}/INDEX
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%{rlibdir}/%{packname}/NAMESPACE
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%{rlibdir}/%{packname}/Meta
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%{rlibdir}/%{packname}/R
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%{rlibdir}/%{packname}/help
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%changelog
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* Tue Apr 05 2011 Adam Huffman <[email protected]> 1.0-1
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- initial package for Fedora

‎R-DESeq.spec

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%global packname DESeq
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%global rlibdir %{_libdir}/R/library
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Name: R-%{packname}
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Version: 1.5.0
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Release: 1%{?dist}
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Summary: Digital gene expresion analysis based on the negative bi
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Group: Applications/Engineering
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License: GPL (>= 3)
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URL: http://bioconductor.org/packages/release/bioc/html/DESeq.html
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Source0: http://bioconductor.org/packages/release/bioc/src/contrib/%{packname}_%{version}.tar.gz
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BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
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Requires: R-Biobase R-locfit
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BuildRequires: R-devel tex(latex) R-Biobase R-locfit R-genefilter R-geneplotter
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BuildRequires: R-xtable R-RColorBrewer
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%description
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Estimate variance-mean dependence in count data from high-throughput
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sequencing assays and test for differential expression based on a model
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using the negative binomial distribution
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%prep
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%setup -q -c -n %{packname}
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%build
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%install
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rm -rf %{buildroot}
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mkdir -p %{buildroot}%{rlibdir}
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%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname}
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test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
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rm -f %{buildroot}%{rlibdir}/R.css
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%check
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%{_bindir}/R CMD check %{packname}
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%clean
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rm -rf %{buildroot}
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%files
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%defattr(-, root, root, -)
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%dir %{rlibdir}/%{packname}
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%doc %{rlibdir}/%{packname}/doc
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%doc %{rlibdir}/%{packname}/html
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%doc %{rlibdir}/%{packname}/DESCRIPTION
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%doc %{rlibdir}/%{packname}/NEWS
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%doc %{rlibdir}/%{packname}/CITATION
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%{rlibdir}/%{packname}/INDEX
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%{rlibdir}/%{packname}/NAMESPACE
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%{rlibdir}/%{packname}/Meta
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%{rlibdir}/%{packname}/R
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%{rlibdir}/%{packname}/help
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%{rlibdir}/%{packname}/libs
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%{rlibdir}/%{packname}/extra
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%changelog
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* Tue Apr 19 2011 Adam Huffman <[email protected]> 1.5.0-1
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- initial package for Fedora

‎R-RBGL.spec

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%global packname RBGL
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%global rlibdir %{_libdir}/R/library
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Name: R-%{packname}
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Version: 1.26.0
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Release: 1%{?dist}
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Summary: An interface to the boost graph library
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Group: Applications/Engineering
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License: Artistic-2.0
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URL: http://cran.r-project.org/web/packages/RBGL/index.html
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Source0: http://cran.r-project.org/src/contrib/RBGL_1.26.0.tar.gz
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BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
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Requires: R-graph R-methods
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Requires: R-Rgraphviz
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BuildRequires: R-devel tex(latex) R-graph R-methods
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%description
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A fairly extensive and comprehensive interface to the graph algorithms
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contained in the BOOST library.
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%prep
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%setup -q -c -n %{packname}
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%build
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%install
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rm -rf %{buildroot}
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mkdir -p %{buildroot}%{rlibdir}
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%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname}
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test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
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rm -f %{buildroot}%{rlibdir}/R.css
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%check
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#%{_bindir}/R CMD check %{packname}
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%clean
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rm -rf %{buildroot}
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%files
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%defattr(-, root, root, -)
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%dir %{rlibdir}/%{packname}
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%doc %{rlibdir}/%{packname}/doc
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%doc %{rlibdir}/%{packname}/html
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%doc %{rlibdir}/%{packname}/DESCRIPTION
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%doc %{rlibdir}/%{packname}/NEWS
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%{rlibdir}/%{packname}/INDEX
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%{rlibdir}/%{packname}/NAMESPACE
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%{rlibdir}/%{packname}/Meta
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%{rlibdir}/%{packname}/R
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%{rlibdir}/%{packname}/help
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%{rlibdir}/%{packname}/XML
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%{rlibdir}/%{packname}/boostExamples
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%{rlibdir}/%{packname}/demos
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%{rlibdir}/%{packname}/dot
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%{rlibdir}/%{packname}/dtd
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%{rlibdir}/%{packname}/fdep.ps
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%{rlibdir}/%{packname}/libs
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%{rlibdir}/%{packname}/data
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%changelog
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* Wed Apr 20 2011 Adam Huffman <[email protected]> 1.26.0-1
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- initial package for Fedora

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