%global packname Rsamtools %global rlibdir %{_libdir}/R/library %global __suggests_exclude ^R\\((BSgenome\\.Hsapiens\\.UCSC\\.hg19|BiocStyle|GenomicFeatures|KEGG\\.db|RNAseqData\\.HNRNPC\\.bam\\.chr14|ShortRead|TxDb\\.Dmelanogaster\\.UCSC\\.dm3\\.ensGene|TxDb\\.Hsapiens\\.UCSC\\.hg18\\.knownGene|graph)\\) Name: R-%{packname} Version: 2.18.0 Release: 2%{dist} Summary: R interface to samtools 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: 0001-format-security-fix.patch BuildRequires: R-devel >= 3.5.0 tex(latex) R-methods R-IRanges-devel >= 2.13.12 BuildRequires: R-GenomicRanges >= 1.31.8 R-Biostrings-devel >= 2.47.6 BuildRequires: R-BiocGenerics >= 0.25.1 R-bitops R-XVector-devel >= 0.19.7 BuildRequires: R-Rhtslib-devel >= 1.17.7 R-GenomeInfoDb >= 1.1.3 BuildRequires: R-S4Vectors-devel >= 0.17.25 R-utils R-BiocParallel R-stats BuildRequires: libcurl-devel Provides: R-Rsamtools-devel = %{version}-%{release} Obsoletes: R-Rsamtools-devel <= 1.34.1 %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. %prep %setup -q -c -n %{packname} pushd %{packname} %patch -P0 -p1 popd sed -i 's|zlibbioc, ||g' %{packname}/DESCRIPTION sed -i '/import(zlibbioc)/d' %{packname}/NAMESPACE %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 %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/ %{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}/extdata/ %{rlibdir}/%{packname}/help/ %{rlibdir}/%{packname}/scripts/ %{rlibdir}/%{packname}/unitTests/ %{rlibdir}/%{packname}/libs/ %changelog * Wed Jul 17 2024 Fedora Release Engineering - 2.18.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild * Fri Apr 26 2024 Iñaki Úcar - 2.18.0-1 - Update to latest version * Thu Apr 25 2024 Iñaki Úcar - 2.12.0-8 - R-maint-sig mass rebuild * Sat Apr 20 2024 Miroslav Suchý - 2.12.0-7 - convert license to SPDX * Mon Jan 22 2024 Fedora Release Engineering - 2.12.0-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Fri Jan 19 2024 Fedora Release Engineering - 2.12.0-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Wed Jul 19 2023 Fedora Release Engineering - 2.12.0-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild * Fri Apr 21 2023 Iñaki Úcar - 2.12.0-3 - R-maint-sig mass rebuild * Wed Jan 18 2023 Fedora Release Engineering - 2.12.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Sat Sep 3 2022 Tom Callaway - 2.12.0-1 - update to 2.12.0 - rebuild for R 4.2.1 * Wed Jul 20 2022 Fedora Release Engineering - 2.8.0-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Wed Jan 19 2022 Fedora Release Engineering - 2.8.0-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Wed Jul 21 2021 Fedora Release Engineering - 2.8.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Wed Jun 16 2021 Tom Callaway - 2.8.0-1 - update to 2.8.0 - Rebuilt for R 4.1.0 * Thu Feb 4 2021 Tom Callaway - 2.6.0-1 - update to 2.6.0 * Mon Jan 25 2021 Fedora Release Engineering - 2.4.0-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Mon Jul 27 2020 Fedora Release Engineering - 2.4.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Mon Jun 8 2020 Tom Callaway - 2.4.0-1 - update to 2.4.0 - rebuild for R 4 * Wed Feb 5 2020 Tom Callaway - 2.2.1-1 - update to 2.2.1 * Tue Jan 28 2020 Fedora Release Engineering - 2.0.3-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Thu Nov 21 2019 Elliott Sales de Andrade - 2.0.3-2 - Exclude Suggests for unavailable packages * Wed Oct 30 2019 Tom Callaway - 2.0.3-1 - update to 2.03 (devel package dies off) * Mon Aug 12 2019 Elliott Sales de Andrade - 1.34.1-3 - Remove explicit dependencies provided by automatic dependency generator * Wed Jul 24 2019 Fedora Release Engineering - 1.34.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild * Thu Feb 7 2019 Tom Callaway - 1.34.1-1 - update to 1.34.1 * Thu Jan 31 2019 Fedora Release Engineering - 1.32.0-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild * Thu Jul 12 2018 Fedora Release Engineering - 1.32.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Thu May 17 2018 Tom Callaway - 1.32.0-1 - update to 1.32.0 * Fri Mar 23 2018 Tom Callaway - 1.30.0-1 - update to 1.30.0 * Wed Feb 07 2018 Fedora Release Engineering - 1.28.0-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Wed Aug 02 2017 Fedora Release Engineering - 1.28.0-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Wed Jul 26 2017 Fedora Release Engineering - 1.28.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Wed May 31 2017 Tom Callaway - 1.28.0-1 - update to 1.28.0 * Fri Feb 10 2017 Fedora Release Engineering - 1.20.2-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Wed Feb 03 2016 Fedora Release Engineering - 1.20.2-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Tue Jun 16 2015 Fedora Release Engineering - 1.20.2-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Fri May 29 2015 Tom Callaway - 1.20.2-1 - update to 1.20.2 - fix DESCRIPTION to not be doc - add -static provide (bz 967213) * Sat May 02 2015 Kalev Lember - 1.16.0-4 - Rebuilt for GCC 5 C++11 ABI change * Fri Aug 15 2014 Fedora Release Engineering - 1.16.0-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild * Sat Jul 19 2014 Ville Skyttä - 1.16.0-2 - Rebuild to fix debuginfo (#1113404) * Mon Jun 9 2014 Tom Callaway - 1.16.0-1 - update to 1.16.0 * Fri Jun 06 2014 Fedora Release Engineering - 1.14.2-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild * Fri Jan 24 2014 Tom Callaway - 1.14.2-1 - update to 1.14.2 * Fri Aug 02 2013 Fedora Release Engineering - 1.12.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild * Thu Apr 11 2013 Tom Callaway - 1.12.0-1 - update to 1.12.0 * 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