%global packname Rsamtools %global rlibdir %{_libdir}/R/library Name: R-%{packname} Version: 1.10.2 Release: 3%{dist} Summary: R interface to samtools Group: Applications/Engineering # Only src/samtools is MIT, and we nuke that in %%prep License: Artistic 2.0 URL: http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html Source0: http://www.bioconductor.org/packages/release/bioc/src/contrib/%{packname}_%{version}.tar.gz Patch0: R-Rsamtools-zlibbioc.patch Patch1: R-Rsamtools-system-samtools.patch Requires: R-core >= 2.8.0 R-methods R-IRanges >= 1.15.35 Requires: R-GenomicRanges >= 1.9.48 R-Biostrings >= 2.25.6 Requires: R-BiocGenerics >= 0.1.3 BuildRequires: R-devel >= 2.8.0 tex(latex) R-methods R-IRanges-devel >= 1.11.26 BuildRequires: R-GenomicRanges >= 1.9.48 R-Biostrings-devel >= 2.25.6 BuildRequires: R-BiocGenerics >= 0.1.3 R-bitops BuildRequires: samtools-devel %description This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), binary variant call (BCF) and compressed indexed tab-delimited (tabix) files. %package devel Summary: Development files for R-Rsamtools Requires: %{name}%{?_isa} = %{version}-%{release} Requires: samtools-devel %description devel Development files for R-Rsamtools. %prep %setup -q -c -n %{packname} %patch0 -p1 -b .zlibbioc %patch1 -p1 -b .system-samtools # Clean out local copy of samtools rm -rf %{packname}/src/samtools/*.h %{packname}/src/samtools/*.c %build %install mkdir -p %{buildroot}%{rlibdir} R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname} test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) rm -f %{buildroot}%{rlibdir}/R.css pushd %{buildroot}%{rlibdir}/%{packname}/include cd samtools for i in /usr/include/samtools/*.h; do ln -s $i . done cd .. cd tabix ln -s /usr/include/samtools/bgzf.h . ln -s /usr/include/samtools/kstring.h . ln -s /usr/include/samtools/knetfile.h . cd .. popd %check # Testing tests optional deps we don't package # _R_CHECK_FORCE_SUGGESTS_=false %%{_bindir}/R CMD check %%{packname} %files %dir %{rlibdir}/%{packname}/ %doc %{rlibdir}/%{packname}/doc/ %doc %{rlibdir}/%{packname}/html/ %doc %{rlibdir}/%{packname}/DESCRIPTION %doc %{rlibdir}/%{packname}/LICENSE %doc %{rlibdir}/%{packname}/NEWS %{rlibdir}/%{packname}/INDEX %{rlibdir}/%{packname}/NAMESPACE %{rlibdir}/%{packname}/Meta/ %{rlibdir}/%{packname}/R/ %{rlibdir}/%{packname}/usretc/ %{rlibdir}/%{packname}/extdata/ %{rlibdir}/%{packname}/help/ %{rlibdir}/%{packname}/scripts/ %{rlibdir}/%{packname}/unitTests/ %{rlibdir}/%{packname}/libs/ %files devel %{rlibdir}/%{packname}/include/ %{rlibdir}/%{packname}/usrlib/ %changelog * Fri Apr 5 2013 Tom Callaway - 1.10.2-3 - add R-bitops as a BuildRequires - fix license tag * Mon Apr 1 2013 Tom Callaway - 1.10.2-2 - cleanup spec (drop unnecessary macro for exec'ing R, unnecessary BR: R) * Fri Feb 22 2013 Tom Callaway - 1.10.2-1 - initial package