%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  polymapR
%global packver   1.1.5
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.1.5
Release:          1%{?dist}%{?buildtag}
Summary:          Linkage Analysis in Outcrossing Polyploids

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


BuildRequires:    R-devel >= 3.5.0
Requires:         R-core >= 3.5.0
BuildArch:        noarch
BuildRequires:    R-CRAN-doParallel 
BuildRequires:    R-CRAN-foreach 
BuildRequires:    R-graphics 
BuildRequires:    R-grDevices 
BuildRequires:    R-CRAN-igraph 
BuildRequires:    R-CRAN-knitr 
BuildRequires:    R-CRAN-MDSMap 
BuildRequires:    R-stats 
BuildRequires:    R-utils 
Requires:         R-CRAN-doParallel 
Requires:         R-CRAN-foreach 
Requires:         R-graphics 
Requires:         R-grDevices 
Requires:         R-CRAN-igraph 
Requires:         R-CRAN-knitr 
Requires:         R-CRAN-MDSMap 
Requires:         R-stats 
Requires:         R-utils 

%description
Creation of linkage maps in polyploid species from marker dosage scores of
an F1 cross from two heterozygous parents. Currently works for outcrossing
diploid, autotriploid, autotetraploid and autohexaploid species, as well
as segmental allotetraploids. Methods are described in a manuscript of
Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>. Since version
1.1.0, both discrete and probabilistic genotypes are acceptable input; for
more details on the latter see Liao et al. (2021)
<doi:10.1007/s00122-021-03834-x>.

%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}