%global packname rtracklayer %global __suggests_exclude ^R\\((BSgenome\\.Hsapiens\\.UCSC\\.hg19|GenomicFeatures|TxDb\\.Hsapiens\\.UCSC\\.hg19\\.knownGene|genefilter|hgu133plus2\\.db|humanStemCell|limma|microRNA|org\\.Hs\\.eg\\.db)\\) Name: R-%{packname} Version: 1.62.0 Release: 3%{dist} Summary: R interface to genome browsers and their annotation tracks # Automatically converted from old format: Artistic 2.0 and BSD - review is highly recommended. License: Artistic-2.0 AND LicenseRef-Callaway-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 Patch0: 0001-fix-format-security.patch Requires: texlive-latex BuildRequires: R-devel >= 3.3.0, R-methods, R-RCurl >= 1.4.2, R-XML >= 1.98.0 BuildRequires: R-IRanges-devel >= 2.13.13, R-GenomicRanges >= 1.37.2, R-Biostrings-devel >= 2.47.6 BuildRequires: R-Rsamtools-devel >= 1.31.2, zlib-devel BuildRequires: R-XVector-devel >= 0.19.7, R-BiocGenerics >= 0.35.3, R-S4Vectors-devel >= 0.23.18 BuildRequires: R-GenomeInfoDb >= 1.15.2, R-GenomicAlignments >= 1.15.6, R-tools BuildRequires: openssl-devel BuildRequires: R-BiocIO, R-restfulr >= 0.0.13 %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 pushd %{packname} %patch -P0 -p1 popd # 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 Sep 04 2024 Miroslav Suchý - 1.62.0-3 - convert license to SPDX * Wed Jul 17 2024 Fedora Release Engineering - 1.62.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild * Fri Apr 26 2024 Iñaki Úcar - 1.62.0-1 - Update to latest version * Thu Apr 25 2024 Iñaki Úcar - 1.56.1-7 - R-maint-sig mass rebuild * Mon Jan 22 2024 Fedora Release Engineering - 1.56.1-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Fri Jan 19 2024 Fedora Release Engineering - 1.56.1-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Wed Jul 19 2023 Fedora Release Engineering - 1.56.1-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild * Fri Apr 21 2023 Iñaki Úcar - 1.56.1-3 - R-maint-sig mass rebuild * Wed Jan 18 2023 Fedora Release Engineering - 1.56.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Sun Sep 04 2022 Iñaki Úcar - 1.56.1-1 - R 4.2.1, update to 1.56.1 * Wed Jul 20 2022 Fedora Release Engineering - 1.52.0-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Wed Jan 19 2022 Fedora Release Engineering - 1.52.0-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Tue Sep 14 2021 Sahana Prasad - 1.52.0-3 - Rebuilt with OpenSSL 3.0.0 * Wed Jul 21 2021 Fedora Release Engineering - 1.52.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Thu Jun 17 2021 Tom Callaway - 1.52.0-1 - update to 1.52.0 - Rebuilt for R 4.1.0 * Thu Feb 4 2021 Tom Callaway - 1.50.0-1 - update to 1.50.0 * Mon Jan 25 2021 Fedora Release Engineering - 1.48.0-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Sat Aug 01 2020 Fedora Release Engineering - 1.48.0-3 - Second attempt - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Mon Jul 27 2020 Fedora Release Engineering - 1.48.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Mon Jun 8 2020 Tom Callaway - 1.48.0-1 - update to 1.48.0 - rebuild for R 4 * Tue Jan 28 2020 Fedora Release Engineering - 1.46.0-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Thu Nov 21 2019 Elliott Sales de Andrade - 1.46.0-2 - Exclude Suggests for unavailable packages * Wed Nov 6 2019 Tom Callaway - 1.46.0-1 - update to 1.46.0 * Mon Aug 12 2019 Elliott Sales de Andrade - 1.44.0-3 - Remove explicit dependencies provided by automatic dependency generator * Wed Jul 24 2019 Fedora Release Engineering - 1.44.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild * Fri Jun 7 2019 Tom Callaway - 1.44.0-1 - update to 1.44.0 * Thu Jan 31 2019 Fedora Release Engineering - 1.40.2-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild * Thu Jul 12 2018 Fedora Release Engineering - 1.40.2-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Fri May 18 2018 Tom Callaway - 1.40.2-1 - update to 1.40.2 * Fri Mar 23 2018 Tom Callaway - 1.38.3-1 - update to 1.38.3 * Wed Feb 07 2018 Fedora Release Engineering - 1.36.3-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Wed Aug 02 2017 Fedora Release Engineering - 1.36.3-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Wed Jul 26 2017 Fedora Release Engineering - 1.36.3-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Wed May 31 2017 Tom Callaway - 1.36.3-1 - update to 1.36.3 * Fri Feb 10 2017 Fedora Release Engineering - 1.30.2-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Thu Feb 11 2016 pingou 1.30.2-1 - Update to version 1.30.2 * Wed Feb 03 2016 Fedora Release Engineering - 1.28.6-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Fri Jul 03 2015 pingou 1.28.6-1 - Update to version 1.28.6 * Tue Jun 16 2015 Fedora Release Engineering - 1.22.3-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Fri Aug 15 2014 Fedora Release Engineering - 1.22.3-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild * Thu Jul 31 2014 Yaakov Selkowitz - 1.22.3-4 - Add missing BR: R-XVector-devel (#1105923) * Thu Jul 03 2014 Pierre-Yves Chibon - 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 - 1.22.3-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild * Mon Feb 3 2014 Tom Callaway - 1.22.3-1 - update to 1.22.3 * Fri Aug 02 2013 Fedora Release Engineering - 1.20.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild * Thu Apr 11 2013 Tom Callaway - 1.20.0-1 - update to 1.20.0 * Fri Feb 22 2013 Tom Callaway - 1.18.2-1 - update to 1.18.2 * Wed Feb 13 2013 Fedora Release Engineering - 1.14.1-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild * Wed Jul 18 2012 Fedora Release Engineering - 1.14.1-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild * Thu Jan 12 2012 Fedora Release Engineering - 1.14.1-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild * 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