%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 1.14.1-2 - update licensing with clarification from Jim Kent * Thu Nov 10 2011 Tom "spot" Callaway 1.14.1-1 - initial package for Fedora