Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild

Signed-off-by: Fedora Release Engineering <releng@fedoraproject.org>

.gitignore

@@ -2,3 +2,8 @@
 /ape_5.1.tar.gz
 /ape_5.2.tar.gz
 /ape_5.3.tar.gz
+/ape_5.4.tar.gz
+/ape_5.4-1.tar.gz
+/ape_5.5.tar.gz
+/ape_5.6-2.tar.gz
+/ape_5.7-1.tar.gz

R-ape.spec

@@ -1,34 +1,32 @@
 %global packname ape
+%global packver  5.7
+%global packrev  1
 %global rlibdir  %{_libdir}/R/library
 
+# Cannot enable until phangorn is added
+%global with_suggests 0
+
+%bcond_with bootstrap
+
 Name:             R-%{packname}
-Version:          5.3
+Version:          %{packver}.%{packrev}
-Release:          1%{?dist}
+Release:          7%{?dist}
 Summary:          Analyses of Phylogenetics and Evolution
 
-License:          GPLv2+
+License:          GPL-2.0-only OR GPL-3.0-only
 URL:              https://CRAN.R-project.org/package=%{packname}
-Source0:          https://cran.r-project.org/src/contrib/%{packname}_%{version}.tar.gz
+Source0:          https://cran.r-project.org/src/contrib/%{packname}_%{packver}-%{packrev}.tar.gz
+
+# https://fedoraproject.org/wiki/Changes/EncourageI686LeafRemoval
+ExcludeArch: %{ix86}
 
 # Here's the R view of the dependencies world:
 # Depends:
-# Imports:   R-nlme, R-lattice, R-graphics, R-methods, R-stats, R-tools, R-utils, R-parallel, R-Rcpp >= 0.12.0
+# Imports:   R-nlme, R-lattice, R-graphics, R-methods, R-stats, R-utils, R-parallel, R-Rcpp >= 0.12.0, R-digest
-# Suggests:  R-gee, R-expm, R-igraph
+# Suggests:  R-gee, R-expm, R-igraph, R-phangorn
-# LinkingTo:
+# LinkingTo: R-Rcpp
 # Enhances:
 
-Requires:         R-nlme
-Requires:         R-lattice
-Requires:         R-graphics
-Requires:         R-methods
-Requires:         R-stats
-Requires:         R-tools
-Requires:         R-utils
-Requires:         R-parallel
-Requires:         R-Rcpp >= 0.12.0
-Suggests:         R-gee
-Suggests:         R-expm
-Suggests:         R-igraph
 BuildRequires:    R-devel
 BuildRequires:    tex(latex)
 BuildRequires:    R-nlme
@@ -36,30 +34,35 @@ BuildRequires:    R-lattice
 BuildRequires:    R-graphics
 BuildRequires:    R-methods
 BuildRequires:    R-stats
-BuildRequires:    R-tools
 BuildRequires:    R-utils
 BuildRequires:    R-parallel
 BuildRequires:    R-Rcpp-devel >= 0.12.0
+BuildRequires:    R-digest
+%if %{without bootstrap}
 BuildRequires:    R-gee
 BuildRequires:    R-expm
 BuildRequires:    R-igraph
+%if %{with_suggests}
+BuildRequires:    R-phangorn
+%endif
+%endif
 
 %description
 Functions for reading, writing, plotting, and manipulating phylogenetic
 trees, analyses of comparative data in a phylogenetic framework, ancestral
 character analyses, analyses of diversification and macroevolution,
 computing distances from DNA sequences, reading and writing nucleotide
-sequences as well as importing from BioConductor, and several tools such
+sequences as well as importing from BioConductor, and several tools such as
-as Mantel's test, generalized skyline plots, graphical exploration of
+Mantel's test, generalized skyline plots, graphical exploration of
 phylogenetic data (alex, trex, kronoviz), estimation of absolute
 evolutionary rates and clock-like trees using mean path lengths and
 penalized likelihood, dating trees with non-contemporaneous sequences,
 translating DNA into AA sequences, and assessing sequence alignments.
 Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and
-triangle methods, and several methods handling incomplete distance
+triangle methods, and several methods handling incomplete distance matrices
-matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some
+(NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call
-functions call external applications (PhyML, Clustal, T-Coffee, Muscle)
+external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are
-whose results are returned into R.
+returned into R.
 
 
 %prep
@@ -77,7 +80,13 @@ rm -f %{buildroot}%{rlibdir}/R.css
 
 
 %check
+%if %{without bootstrap}
+%if %{with_suggests}
 %{_bindir}/R CMD check %{packname}
+%else
+_R_CHECK_FORCE_SUGGESTS_=0 %{_bindir}/R CMD check %{packname} --no-examples
+%endif
+%endif
 
 
 %files
@@ -98,6 +107,93 @@ rm -f %{buildroot}%{rlibdir}/R.css
 
 
 %changelog
+* Wed Jul 17 2024 Fedora Release Engineering <releng@fedoraproject.org> - 5.7.1-7
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild
+
+* Thu Apr 25 2024 Iñaki Úcar <iucar@fedoraproject.org> - 5.7.1-6
+- R-maint-sig mass rebuild
+
+* Mon Jan 22 2024 Fedora Release Engineering <releng@fedoraproject.org> - 5.7.1-5
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
+
+* Fri Jan 19 2024 Fedora Release Engineering <releng@fedoraproject.org> - 5.7.1-4
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
+
+* Wed Jul 19 2023 Fedora Release Engineering <releng@fedoraproject.org> - 5.7.1-3
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild
+
+* Fri Apr 21 2023 Iñaki Úcar <iucar@fedoraproject.org> - 5.7.1-2
+- R-maint-sig mass rebuild
+
+* Mon Mar 13 2023 Tom Callaway <spot@fedoraproject.org> - 5.7.1-1
+- update to 5.7-1
+
+* Sun Jan 22 2023 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 5.6.2-3
+- Drop support for i686
+- Switch to SPDX licenses
+
+* Wed Jan 18 2023 Fedora Release Engineering <releng@fedoraproject.org> - 5.6.2-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild
+
+* Fri Sep  2 2022 Tom Callaway <spot@fedoraproject.org> - 5.6.2-1
+- update to 5.6-2
+- rebuild for R 4.2.1
+- bootstrap on
+
+* Wed Jul 20 2022 Fedora Release Engineering <releng@fedoraproject.org> - 5.5-4
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
+
+* Wed Jan 19 2022 Fedora Release Engineering <releng@fedoraproject.org> - 5.5-3
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
+
+* Wed Jul 21 2021 Fedora Release Engineering <releng@fedoraproject.org> - 5.5-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
+
+* Thu Jun 17 2021 Tom Callaway <spot@fedoraproject.org> - 5.5-2
+- bootstrap off, but rework check logic around missing phangorn
+
+* Tue Jun 15 2021 Tom Callaway <spot@fedoraproject.org> - 5.5-1
+- update to 5.5
+- bootstrap
+- Rebuilt for R 4.1.0
+
+* Mon Jun  7 2021 Tom Callaway <spot@fedoraproject.org> - 5.4.1-3
+- rebuild for R 4.1.0
+
+* Mon Jan 25 2021 Fedora Release Engineering <releng@fedoraproject.org> - 5.4.1-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
+
+* Thu Aug 13 2020 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 5.4.1-1
+- Update to latest version (#1868589)
+
+* Mon Aug 10 2020 Tom Callaway <spot@fedoraproject.org> - 5.4-3
+- rebuild for FlexiBLAS R
+
+* Mon Jul 27 2020 Fedora Release Engineering <releng@fedoraproject.org> - 5.4-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
+
+* Tue Jul 21 2020 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 5.4-1
+- Update to latest version
+
+* Fri Jun  5 2020 Tom Callaway <spot@fedoraproject.org> - 5.3-7
+- rebuild for R 4
+- turnoff bootstrap
+
+* Sun Feb 23 2020 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 5.3-6
+- Add bootstrap setup to build without igraph
+
+* Tue Feb 18 2020 Tom Callaway <spot@fedoraproject.org> - 5.3-5
+- rebuild against R without libRlapack.so
+
+* Tue Jan 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 5.3-4
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
+
+* Sun Aug 11 2019 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 5.3-3
+- Remove explicit dependencies provided by automatic dependency generator
+
+* Wed Jul 24 2019 Fedora Release Engineering <releng@fedoraproject.org> - 5.3-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
+
 * Sun Mar 17 2019 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 5.3-1
 - Update to latest version
 

sources

@@ -1 +1 @@
-SHA512 (ape_5.3.tar.gz) = 82264880c07597880b91ebb94110dcb8c85581fb97f8e8c478075eddbd6490b92488df43a0f3e7b505e8249758c54feeaf5103669c32ce898ff1eff9e22a68cd
+SHA512 (ape_5.7-1.tar.gz) = 15adc701619ff91e139f8f308614fe2abee04cab1a148ac79392b96f51ede6ea731cbdb1ce9d715bd6d927f8dada49767b73bf919b7996e7deb6b6b05d345369