%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  MADPop
%global packver   1.1.7
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.1.7
Release:          1%{?dist}%{?buildtag}
Summary:          MHC Allele-Based Differencing Between Populations

License:          GPL-3
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel >= 3.4.0
Requires:         R-core >= 3.4.0
BuildRequires:    R-CRAN-RcppParallel >= 5.0.1
BuildRequires:    R-CRAN-rstan >= 2.26.0
BuildRequires:    R-CRAN-StanHeaders >= 2.26.0
BuildRequires:    R-CRAN-BH >= 1.66.0
BuildRequires:    R-CRAN-RcppEigen >= 0.3.3.3.0
BuildRequires:    R-CRAN-Rcpp >= 0.12.0
BuildRequires:    R-methods 
BuildRequires:    R-stats 
BuildRequires:    R-CRAN-rstantools 
BuildRequires:    R-CRAN-rstantools
Requires:         R-CRAN-rstan >= 2.26.0
Requires:         R-CRAN-Rcpp >= 0.12.0
Requires:         R-methods 
Requires:         R-stats 
Requires:         R-CRAN-rstantools 
Requires:         R-CRAN-rstantools

%description
Tools for the analysis of population differences using the Major
Histocompatibility Complex (MHC) genotypes of samples having a variable
number of alleles (1-4) recorded for each individual.  A hierarchical
Dirichlet-Multinomial model on the genotype counts is used to pool small
samples from multiple populations for pairwise tests of equality.
Bayesian inference is implemented via the 'rstan' package.  Bootstrapped
and posterior p-values are provided for chi-squared and likelihood ratio
tests of equal genotype probabilities.

%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
[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \
  sed -i 's@-g0@@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}