%global packname rtracklayer
Name: R-%{packname}
Version: 1.14.1
Release: 2%{?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/2.9/bioc/src/contrib/%{packname}_%{version}.tar.gz
Source1: rtracklayer_jimkent_license.txt
Patch0: R-rtracklayer-1.14.1-no-zlibbioc.patch
Requires: R-core >= 2.7.0, texlive-latex, R-methods, R-RCurl >= 1.4.2, R-XML >= 1.98.0
Requires: R-IRanges >= 1.11.34, R-GenomicRanges >= 1.5.42, R-Biostrings >= 2.21.12
Requires: R-BSgenome >= 1.15.17
BuildRequires: R-devel >= 2.7.0, R-methods, R-RCurl >= 1.4.2, R-XML >= 1.98.0
BuildRequires: R-IRanges-devel >= 1.11.34, R-GenomicRanges >= 1.5.42, R-Biostrings-devel >= 2.21.12
BuildRequires: R-BSgenome >= 1.15.17, zlib-devel
%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}
%patch0 -p0 -b .no-zlibbioc
# 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}/DESCRIPTION
%doc %{_libdir}/R/library/%{packname}/doc/
%doc rtracklayer_jimkent_license.txt
%{_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}/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/
%changelog
* 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