File R-ape.spec of Package R-ape

#
# spec file for package R-ape
#
# Copyright (c) 2019 SUSE LINUX GmbH, Nuernberg, Germany.
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
# upon. The license for this file, and modifications and additions to the
# file, is the same license as for the pristine package itself (unless the
# license for the pristine package is not an Open Source License, in which
# case the license is the MIT License). An "Open Source License" is a
# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.

# Please submit bugfixes or comments via https://bugs.opensuse.org/
#


%global packname  ape
%global rlibdir   %{_libdir}/R/library
Name:           R-%{packname}
Version:        5.3
Release:        0
Summary:        Analyses of Phylogenetics and Evolution
License:        GPL (>= 2)
URL:            http://cran.r-project.org/web/packages/%{packname}
Source:         http://cran.r-project.org/src/contrib/%{packname}_%{version}.tar.gz
BuildRequires:  R-Rcpp-devel
BuildRequires:  R-Rcpp-devel >= 0.12.0
BuildRequires:  R-base-devel
BuildRequires:  R-graphics
BuildRequires:  R-lattice
BuildRequires:  R-methods
BuildRequires:  R-nlme
BuildRequires:  R-parallel
BuildRequires:  R-stats
BuildRequires:  R-tools
BuildRequires:  R-utils
BuildRequires:  fdupes
BuildRequires:  gcc
BuildRequires:  gcc-c++
BuildRequires:  gcc-fortran
BuildRequires:  texinfo
Requires:       R-Rcpp
Requires:       R-Rcpp >= 0.12.0
Requires:       R-base
Requires:       R-graphics
Requires:       R-lattice
Requires:       R-methods
Requires:       R-nlme
Requires:       R-parallel
Requires:       R-stats
Requires:       R-tools
Requires:       R-utils
%if 0%{?sle_version} > 120400 || 0%{?is_opensuse}
# Three others commonly needed
BuildRequires:  tex(ae.sty)
BuildRequires:  tex(fancyvrb.sty)
BuildRequires:  tex(inconsolata.sty)
BuildRequires:  tex(natbib.sty)
%else
BuildRequires:  texlive
%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
as 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
matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some
functions call external applications (PhyML, Clustal, T-Coffee, Muscle)
whose results are returned into R.

%prep
%setup -q -c -n %{packname}
find %{packname}/src \( -name '*.a' -or -name '*.o' -or -name '*.so' -or -name '*.lo' -or -name '*.la' \) -print -delete

%build

%install
mkdir -p %{buildroot}%{rlibdir}
%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname}
find %{packname}/src \( -name '*.a' -or -name '*.o' -or -name '*.so' -or -name '*.lo' -or -name '*.la' \) -delete
rm -f %{buildroot}%{rlibdir}/R.css
%fdupes %{buildroot}%{rlibdir}/%{packname}


%files
%dir %{rlibdir}/%{packname}
%doc %{rlibdir}/ape/CITATION
%doc %{rlibdir}/ape/doc
%doc %{rlibdir}/ape/html
%doc %{rlibdir}/ape/NEWS
%{rlibdir}/ape/NAMESPACE
%{rlibdir}/ape/Meta
%{rlibdir}/ape/libs
%{rlibdir}/ape/DESCRIPTION
%{rlibdir}/ape/help
%{rlibdir}/ape/R
%{rlibdir}/ape/data
%{rlibdir}/ape/INDEX

%changelog