%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  updog
%global packver   2.1.4
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          2.1.4
Release:          1%{?dist}%{?buildtag}
Summary:          Flexible Genotyping for Polyploids

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-Rcpp >= 0.12.16
BuildRequires:    R-CRAN-RcppArmadillo 
BuildRequires:    R-CRAN-assertthat 
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-CRAN-reshape2 
BuildRequires:    R-CRAN-foreach 
BuildRequires:    R-CRAN-future 
BuildRequires:    R-CRAN-doFuture 
BuildRequires:    R-CRAN-doRNG 
BuildRequires:    R-methods 
BuildRequires:    R-CRAN-iterators 
Requires:         R-CRAN-Rcpp >= 0.12.16
Requires:         R-CRAN-RcppArmadillo 
Requires:         R-CRAN-assertthat 
Requires:         R-CRAN-ggplot2 
Requires:         R-CRAN-reshape2 
Requires:         R-CRAN-foreach 
Requires:         R-CRAN-future 
Requires:         R-CRAN-doFuture 
Requires:         R-CRAN-doRNG 
Requires:         R-methods 
Requires:         R-CRAN-iterators 

%description
Implements empirical Bayes approaches to genotype polyploids from next
generation sequencing data while accounting for allele bias,
overdispersion, and sequencing error. The main functions are flexdog() and
multidog(), which allow the specification of many different genotype
distributions. Also provided are functions to simulate genotypes, rgeno(),
and read-counts, rflexdog(), as well as functions to calculate oracle
genotyping error rates, oracle_mis(), and correlation with the true
genotypes, oracle_cor(). These latter two functions are useful for read
depth calculations. Run browseVignettes(package = "updog") in R for
example usage. See Gerard et al. (2018) <doi:10.1534/genetics.118.301468>
and Gerard and Ferrao (2020) <doi:10.1093/bioinformatics/btz852> for
details on the implemented methods.

%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}