%global __brp_check_rpaths %{nil}
%global packname  BeastJar
%global packver   1.10.6
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.10.6
Release:          1%{?dist}%{?buildtag}
Summary:          JAR Dependency for MCMC Using 'BEAST'

License:          Apache License 2.0
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel
Requires:         R-core
BuildArch:        noarch
BuildRequires:    R-CRAN-rJava 
Requires:         R-CRAN-rJava 

%description
Provides JAR to perform Markov chain Monte Carlo (MCMC) inference using
the popular Bayesian Evolutionary Analysis by Sampling Trees 'BEAST'
software library of Suchard et al (2018) <doi:10.1093/ve/vey016>. 'BEAST'
supports auto-tuning Metropolis-Hastings, slice, Hamiltonian Monte Carlo
and Sequential Monte Carlo sampling for a large variety of composable
standard and phylogenetic statistical models using high performance
computing.  By placing the 'BEAST' JAR in this package, we offer an
efficient distribution system for 'BEAST' use by other R packages using
CRAN.

%prep
%setup -q -c -n %{packname}

# fix end of executable files
find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \;
# prevent binary stripping
[ -d %{packname}/src ] && find %{packname}/src -type f -exec \
  sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true
# don't allow local prefix in executable scripts
find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \;

%build

%install

mkdir -p %{buildroot}%{rlibdir}
%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname}
test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
rm -f %{buildroot}%{rlibdir}/R.css
# remove buildroot from installed files
find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \;

%files
%{rlibdir}/%{packname}