%global packname rtracklayer
Name: R-%{packname}
Version: 1.36.3
Release: 1%{dist}
Summary: R interface to genome browsers and their annotation tracks
Group: Applications/Productivity
License: Artistic 2.0 and BSD
URL: http://www.bioconductor.org/packages/release/bioc/html/rtracklayer.html
Source0: http://www.bioconductor.org/packages/release/bioc/src/contrib/%{packname}_%{version}.tar.gz
Source1: rtracklayer_jimkent_license.txt
Requires: R-core >= 3.3.0, texlive-latex, R-methods, R-RCurl >= 1.4.2, R-XML >= 1.98.0
Requires: R-IRanges >= 2.3.7, R-GenomicRanges >= 1.21.20, R-Biostrings >= 2.43.7
Requires: R-BSgenome >= 1.15.17, R-Rsamtools >= 1.17.8, R-XVector >= 0.9.4
Requires: R-BiocGenerics >= 0.13.8, R-S4Vectors >= 0.13.13, R-GenomeInfoDb >= 1.3.14
Requires: R-GenomicAlignments >= 1.5.4, R-tools
BuildRequires: R-devel >= 3.3.0, R-methods, R-RCurl >= 1.4.2, R-XML >= 1.98.0
BuildRequires: R-IRanges-devel >= 2.3.7, R-GenomicRanges >= 1.21.20, R-Biostrings-devel >= 2.43.7
BuildRequires: R-BSgenome >= 1.23.1, R-Rsamtools-devel >= 1.17.8, zlib-devel
BuildRequires: R-XVector-devel >= 0.9.4, R-BiocGenerics >= 0.13.8, R-S4Vectors-devel >= 0.13.13
BuildRequires: R-GenomeInfoDb >= 1.3.14, R-GenomicAlignments >= 1.5.4, R-tools
%description
Extensible framework for interacting with multiple genome browsers (currently
UCSC built-in) and manipulating annotation tracks in various formats
(currently GFF, BED, bedGraph, BED15, WIG, and BigWig built-in). The user may
export/import tracks to/from the supported browsers, as well as query and
modify the browser state, such as the current viewport.
%prep
%setup -c -q -n %{packname}
sed -i -e 's|zlibbioc,||' rtracklayer/DESCRIPTION
sed -i -e 's|import(zlibbioc)||' rtracklayer/NAMESPACE
# This email confirms that we have permission to use the Jim Kent
# copyrighted files under the BSD license.
cp %{SOURCE1} .
%build
%install
mkdir -p %{buildroot}%{_libdir}/R/library
%{_bindir}/R CMD INSTALL %{packname} -l %{buildroot}%{_libdir}/R/library
# Clean up in advance of check
test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
rm -rf %{buildroot}%{_libdir}/R/library/R.css
# Zero file
rm -rf %{buildroot}%{_libdir}/R/library/%{packname}/tests/quickload/T_species_Oct_2011/bedGraphData.bw
%check
# All sorts of missing Suggests prevents this from working.
# %%{_bindir}/R CMD check %%{packname}
%files
%dir %{_libdir}/R/library/%{packname}
%doc %{_libdir}/R/library/%{packname}/html
%doc %{_libdir}/R/library/%{packname}/CITATION
%doc %{_libdir}/R/library/%{packname}/DESCRIPTION
%doc %{_libdir}/R/library/%{packname}/NEWS
%doc %{_libdir}/R/library/%{packname}/doc/
%license rtracklayer_jimkent_license.txt
%license %{_libdir}/R/library/%{packname}/LICENSE
%{_libdir}/R/library/%{packname}/INDEX
%{_libdir}/R/library/%{packname}/NAMESPACE
%{_libdir}/R/library/%{packname}/Meta
%{_libdir}/R/library/%{packname}/R
%{_libdir}/R/library/%{packname}/data/
%{_libdir}/R/library/%{packname}/extdata/
%{_libdir}/R/library/%{packname}/demo/
%{_libdir}/R/library/%{packname}/help
%{_libdir}/R/library/%{packname}/libs/
%{_libdir}/R/library/%{packname}/notes/
%{_libdir}/R/library/%{packname}/scripts/
%{_libdir}/R/library/%{packname}/tests/
%{_libdir}/R/library/%{packname}/unitTests/
%changelog
* Wed May 31 2017 Tom Callaway <spot@fedoraproject.org> - 1.36.3-1
- update to 1.36.3
* Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.30.2-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
* Thu Feb 11 2016 pingou <pingou@pingoured.fr> 1.30.2-1
- Update to version 1.30.2
* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 1.28.6-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
* Fri Jul 03 2015 pingou <pingou@pingoured.fr> 1.28.6-1
- Update to version 1.28.6
* Tue Jun 16 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.22.3-6
- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
* Fri Aug 15 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.22.3-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
* Thu Jul 31 2014 Yaakov Selkowitz <yselkowi@redhat.com> - 1.22.3-4
- Add missing BR: R-XVector-devel (#1105923)
* Thu Jul 03 2014 Pierre-Yves Chibon <pingou@pingoured.fr> - 1.22.3-3
- Drop the patch fixing the zlibbioc import/dependency in favor of a couple of
sed commands
* Fri Jun 06 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.22.3-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
* Mon Feb 3 2014 Tom Callaway <spot@fedoraproject.org> - 1.22.3-1
- update to 1.22.3
* Fri Aug 02 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.20.0-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
* Thu Apr 11 2013 Tom Callaway <spot@fedoraproject.org> - 1.20.0-1
- update to 1.20.0
* Fri Feb 22 2013 Tom Callaway <spot@fedoraproject.org> - 1.18.2-1
- update to 1.18.2
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.14.1-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
* Wed Jul 18 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.14.1-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
* Thu Jan 12 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.14.1-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild
* Mon Nov 14 2011 Tom Callaway <spot@fedoraproject.org> 1.14.1-2
- update licensing with clarification from Jim Kent
* Thu Nov 10 2011 Tom "spot" Callaway <tcallawa@redhat.com> 1.14.1-1
- initial package for Fedora