%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  ldsep
%global packver   2.1.5
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          2.1.5
Release:          1%{?dist}%{?buildtag}
Summary:          Linkage Disequilibrium Shrinkage Estimation for Polyploids

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


BuildRequires:    R-devel >= 2.10
Requires:         R-core >= 2.10
BuildRequires:    R-CRAN-Rcpp 
BuildRequires:    R-CRAN-foreach 
BuildRequires:    R-CRAN-doParallel 
BuildRequires:    R-CRAN-ashr 
BuildRequires:    R-CRAN-corrplot 
BuildRequires:    R-CRAN-lpSolve 
BuildRequires:    R-CRAN-abind 
BuildRequires:    R-CRAN-modeest 
BuildRequires:    R-CRAN-matrixStats 
BuildRequires:    R-CRAN-RcppArmadillo 
Requires:         R-CRAN-Rcpp 
Requires:         R-CRAN-foreach 
Requires:         R-CRAN-doParallel 
Requires:         R-CRAN-ashr 
Requires:         R-CRAN-corrplot 
Requires:         R-CRAN-lpSolve 
Requires:         R-CRAN-abind 
Requires:         R-CRAN-modeest 
Requires:         R-CRAN-matrixStats 

%description
Estimate haplotypic or composite pairwise linkage disequilibrium (LD) in
polyploids, using either genotypes or genotype likelihoods. Support is
provided to estimate the popular measures of LD: the LD coefficient D, the
standardized LD coefficient D', and the Pearson correlation coefficient r.
All estimates are returned with corresponding standard errors. These
estimates and standard errors can then be used for shrinkage estimation.
The main functions are ldfast(), ldest(), mldest(), sldest(), plot.lddf(),
format_lddf(), and ldshrink(). Details of the methods are available in
Gerard (2021a) <doi:10.1111/1755-0998.13349> and Gerard (2021b)
<doi:10.1038/s41437-021-00462-5>.

%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}