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%global packname Rsamtools
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%global rlibdir %{_libdir}/R/library
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Name: R-%{packname}
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Version: 1.20.2
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Release: 4%{dist}
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Summary: R interface to samtools
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Group: Applications/Engineering
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# Only src/samtools is MIT, and we nuke that in %%prep
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License: Artistic 2.0
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URL: http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html
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Source0: http://www.bioconductor.org/packages/release/bioc/src/contrib/%{packname}_%{version}.tar.gz
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Patch0: R-Rsamtools-zlibbioc.patch
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Patch1: R-Rsamtools-system-samtools.patch
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Requires: R-core >= 3.0.0 R-methods R-IRanges >= 1.99.17
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Requires: R-GenomicRanges >= 1.17.19 R-Biostrings >= 2.33.11
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Requires: R-BiocGenerics >= 0.1.3 R-XVector >= 0.5.3
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Requires: R-GenomeInfoDb >= 1.1.3
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Requires: R-S4Vectors >= 0.5.11
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BuildRequires: R-devel >= 3.0.0 tex(latex) R-methods R-IRanges-devel >= 1.99.17
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BuildRequires: R-GenomicRanges >= 1.17.19 R-Biostrings-devel >= 2.33.11
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BuildRequires: R-BiocGenerics >= 0.1.3 R-bitops R-XVector-devel >= 0.5.3
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BuildRequires: samtools-devel >= 0.1.19-7 R-GenomeInfoDb >= 1.1.3
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BuildRequires: R-S4Vectors-devel >= 0.5.11
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%description
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This package provides an interface to the 'samtools', 'bcftools',
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and 'tabix' utilities (see 'LICENCE') for manipulating SAM
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(Sequence Alignment / Map), binary variant call (BCF) and
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compressed indexed tab-delimited (tabix) files.
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%package devel
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Summary: Development files for R-Rsamtools
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Requires: %{name}%{?_isa} = %{version}-%{release}
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Requires: samtools-devel
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Provides: %{name}-static = %{version}-%{release}
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%description devel
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Development files for R-Rsamtools.
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%prep
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%setup -q -c -n %{packname}
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%patch0 -p1 -b .zlibbioc
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%patch1 -p1 -b .system-samtools
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# Clean out local copy of samtools
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rm -rf %{packname}/src/samtools/*.h %{packname}/src/samtools/*.c
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%build
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%install
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mkdir -p %{buildroot}%{rlibdir}
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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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pushd %{buildroot}%{rlibdir}/%{packname}/include
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cd samtools
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for i in /usr/include/samtools/*.h; do
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ln -s $i .
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done
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cd ..
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cd tabix
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ln -s /usr/include/samtools/bgzf.h .
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ln -s /usr/include/samtools/kstring.h .
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ln -s /usr/include/samtools/knetfile.h .
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cd ..
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popd
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%check
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# Testing tests optional deps we don't package
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# _R_CHECK_FORCE_SUGGESTS_=false %%{_bindir}/R CMD check %%{packname}
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%files
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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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%{rlibdir}/%{packname}/DESCRIPTION
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%doc %{rlibdir}/%{packname}/LICENSE
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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}/extdata/
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%{rlibdir}/%{packname}/help/
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%{rlibdir}/%{packname}/scripts/
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%{rlibdir}/%{packname}/unitTests/
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%{rlibdir}/%{packname}/libs/
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%files devel
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%{rlibdir}/%{packname}/include/
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%{rlibdir}/%{packname}/usrlib/
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%changelog
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* Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.20.2-4
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
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* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 1.20.2-3
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
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* Tue Jun 16 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.20.2-2
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
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bdcf08e |
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* Fri May 29 2015 Tom Callaway <spot@fedoraproject.org> - 1.20.2-1
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- update to 1.20.2
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- fix DESCRIPTION to not be doc
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- add -static provide (bz 967213)
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* Sat May 02 2015 Kalev Lember <kalevlember@gmail.com> - 1.16.0-4
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- Rebuilt for GCC 5 C++11 ABI change
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* Fri Aug 15 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.16.0-3
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
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fc4c97b |
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* Sat Jul 19 2014 Ville Skyttä <ville.skytta@iki.fi> - 1.16.0-2
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- Rebuild to fix debuginfo (#1113404)
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8fcdf6e |
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* Mon Jun 9 2014 Tom Callaway <spot@fedoraproject.org> - 1.16.0-1
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- update to 1.16.0
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* Fri Jun 06 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.14.2-2
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
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c1c613f |
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* Fri Jan 24 2014 Tom Callaway <spot@fedoraproject.org> - 1.14.2-1
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1cce5e4 |
- update to 1.14.2
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1cce5e4 |
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7d60ef0 |
* Fri Aug 02 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.12.0-2
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
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7d60ef0 |
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77f1406 |
* Thu Apr 11 2013 Tom Callaway <spot@fedoraproject.org> - 1.12.0-1
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77f1406 |
- update to 1.12.0
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77f1406 |
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* Fri Apr 5 2013 Tom Callaway <spot@fedoraproject.org> - 1.10.2-3
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- add R-bitops as a BuildRequires
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- fix license tag
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* Mon Apr 1 2013 Tom Callaway <spot@fedoraproject.org> - 1.10.2-2
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- cleanup spec (drop unnecessary macro for exec'ing R, unnecessary BR: R)
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* Fri Feb 22 2013 Tom Callaway <spot@fedoraproject.org> - 1.10.2-1
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- initial package
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