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%global packname rtracklayer
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Name: R-%{packname}
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Version: 1.28.6
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Release: 1%{dist}
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Summary: R interface to genome browsers and their annotation tracks
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Group: Applications/Productivity
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License: Artistic 2.0 and BSD
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URL: http://www.bioconductor.org/packages/release/bioc/html/rtracklayer.html
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Source0: http://www.bioconductor.org/packages/2.9/bioc/src/contrib/%{packname}_%{version}.tar.gz
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Source1: rtracklayer_jimkent_license.txt
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Requires: R-core >= 3.0.0, texlive-latex, R-methods, R-RCurl >= 1.4.2, R-XML >= 1.98.0
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Requires: R-IRanges >= 1.19.34, R-GenomicRanges >= 1.13.43, R-Biostrings >= 2.29.18
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Requires: R-BSgenome >= 1.15.17, R-Rsamtools >= 1.13.1, R-XVector >= 0.1.3
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BuildRequires: R-devel >= 3.0.0, R-methods, R-RCurl >= 1.4.2, R-XML >= 1.98.0
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BuildRequires: R-IRanges-devel >= 1.19.34, R-GenomicRanges >= 1.13.43, R-Biostrings-devel >= 2.29.18
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BuildRequires: R-BSgenome >= 1.23.1, R-Rsamtools-devel >= 1.13.1, zlib-devel
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Yaakov Selkowitz |
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BuildRequires: R-XVector-devel >= 0.1.3
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%description
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Extensible framework for interacting with multiple genome browsers (currently
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UCSC built-in) and manipulating annotation tracks in various formats
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(currently GFF, BED, bedGraph, BED15, WIG, and BigWig built-in). The user may
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export/import tracks to/from the supported browsers, as well as query and
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modify the browser state, such as the current viewport.
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%prep
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%setup -c -q -n %{packname}
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sed -i -e 's|zlibbioc,||' rtracklayer/DESCRIPTION
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sed -i -e 's|import(zlibbioc)||' rtracklayer/NAMESPACE
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# This email confirms that we have permission to use the Jim Kent
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# copyrighted files under the BSD license.
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cp %{SOURCE1} .
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%build
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%install
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mkdir -p %{buildroot}%{_libdir}/R/library
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%{_bindir}/R CMD INSTALL %{packname} -l %{buildroot}%{_libdir}/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}%{_libdir}/R/library/R.css
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# Zero file
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rm -rf %{buildroot}%{_libdir}/R/library/%{packname}/tests/quickload/T_species_Oct_2011/bedGraphData.bw
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%check
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# All sorts of missing Suggests prevents this from working.
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# %%{_bindir}/R CMD check %%{packname}
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%files
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%dir %{_libdir}/R/library/%{packname}
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%doc %{_libdir}/R/library/%{packname}/html
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%doc %{_libdir}/R/library/%{packname}/CITATION
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%doc %{_libdir}/R/library/%{packname}/DESCRIPTION
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%doc %{_libdir}/R/library/%{packname}/NEWS
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%doc %{_libdir}/R/library/%{packname}/doc/
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%doc rtracklayer_jimkent_license.txt
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%{_libdir}/R/library/%{packname}/INDEX
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%{_libdir}/R/library/%{packname}/NAMESPACE
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%{_libdir}/R/library/%{packname}/Meta
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%{_libdir}/R/library/%{packname}/R
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%{_libdir}/R/library/%{packname}/data/
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%{_libdir}/R/library/%{packname}/extdata/
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%{_libdir}/R/library/%{packname}/demo/
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%{_libdir}/R/library/%{packname}/help
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%{_libdir}/R/library/%{packname}/libs/
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%{_libdir}/R/library/%{packname}/notes/
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%{_libdir}/R/library/%{packname}/scripts/
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%{_libdir}/R/library/%{packname}/tests/
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%{_libdir}/R/library/%{packname}/unitTests/
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%changelog
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* Fri Jul 03 2015 pingou <pingou@pingoured.fr> 1.28.6-1
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- Update to version 1.28.6
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* Tue Jun 16 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.22.3-6
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
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* Fri Aug 15 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.22.3-5
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
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8d95ff1 |
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Yaakov Selkowitz |
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* Thu Jul 31 2014 Yaakov Selkowitz <yselkowi@redhat.com> - 1.22.3-4
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Yaakov Selkowitz |
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- Add missing BR: R-XVector-devel (#1105923)
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Yaakov Selkowitz |
080be86 |
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* Thu Jul 03 2014 Pierre-Yves Chibon <pingou@pingoured.fr> - 1.22.3-3
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- Drop the patch fixing the zlibbioc import/dependency in favor of a couple of
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sed commands
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* Fri Jun 06 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.22.3-2
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
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* Mon Feb 3 2014 Tom Callaway <spot@fedoraproject.org> - 1.22.3-1
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- update to 1.22.3
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* Fri Aug 02 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.20.0-2
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
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0a80b55 |
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* Thu Apr 11 2013 Tom Callaway <spot@fedoraproject.org> - 1.20.0-1
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- update to 1.20.0
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* Fri Feb 22 2013 Tom Callaway <spot@fedoraproject.org> - 1.18.2-1
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- update to 1.18.2
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d6b1cad |
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.14.1-5
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d6b1cad |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
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d6b1cad |
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* Wed Jul 18 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.14.1-4
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
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* Thu Jan 12 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.14.1-3
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild
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* Mon Nov 14 2011 Tom Callaway <spot@fedoraproject.org> 1.14.1-2
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- update licensing with clarification from Jim Kent
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* Thu Nov 10 2011 Tom "spot" Callaway <tcallawa@redhat.com> 1.14.1-1
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- initial package for Fedora
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