%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  HardyWeinberg
%global packver   1.7.8
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.7.8
Release:          1%{?dist}%{?buildtag}
Summary:          Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

License:          GPL (>= 2)
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel >= 1.8.0
Requires:         R-core >= 1.8.0
BuildRequires:    R-CRAN-mice 
BuildRequires:    R-CRAN-nnet 
BuildRequires:    R-CRAN-Rsolnp 
BuildRequires:    R-CRAN-shape 
BuildRequires:    R-CRAN-Rcpp 
Requires:         R-CRAN-mice 
Requires:         R-CRAN-nnet 
Requires:         R-CRAN-Rsolnp 
Requires:         R-CRAN-shape 
Requires:         R-CRAN-Rcpp 

%description
Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908;
Weinberg, 1908) for bi and multi-allelic genetic marker data. All
classical tests (chi-square, exact, likelihood-ratio and permutation
tests) with bi-allelic variants are included in the package, as well as
functions for power computation and for the simulation of marker data
under equilibrium and disequilibrium. Routines for dealing with markers on
the X-chromosome are included (Graffelman & Weir, 2016)
<doi:10.1038/hdy.2016.20>, including Bayesian procedures. Some exact and
permutation procedures also work with multi-allelic variants. Special test
procedures that jointly address Hardy-Weinberg equilibrium and equality of
allele frequencies in both sexes are supplied, for the bi and
multi-allelic case. Functions for testing equilibrium in the presence of
missing data by using multiple imputation are also provided. Implements
several graphics for exploring the equilibrium status of a large set of
bi-allelic markers: ternary plots with acceptance regions, log-ratio plots
and Q-Q plots. The functionality of the package is explained in detail in
a related JSS paper <doi:10.18637/jss.v064.i03>.

%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}