%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  extBatchMarking
%global packver   1.1.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.1.0
Release:          1%{?dist}%{?buildtag}
Summary:          Extended Batch Marking Models

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


BuildRequires:    R-devel >= 4.0
Requires:         R-core >= 4.0
BuildRequires:    R-CRAN-doParallel 
BuildRequires:    R-CRAN-foreach 
BuildRequires:    R-CRAN-optimbase 
BuildRequires:    R-CRAN-Rcpp 
BuildRequires:    R-parallel 
BuildRequires:    R-CRAN-RcppArmadillo 
Requires:         R-CRAN-doParallel 
Requires:         R-CRAN-foreach 
Requires:         R-CRAN-optimbase 
Requires:         R-CRAN-Rcpp 
Requires:         R-parallel 

%description
A system for batch-marking data analysis to estimate survival
probabilities, capture probabilities, and enumerate the population
abundance for both marked and unmarked individuals. The estimation of only
marked individuals can be achieved through the batchMarkOptim() function.
Similarly, the combined marked and unmarked can be achieved through the
batchMarkUnmarkOptim() function. The algorithm was also implemented for
the hidden Markov model encapsulated in batchMarkUnmarkOptim() to estimate
the abundance of both marked and unmarked individuals in the population.
The package is based on the paper: "Hidden Markov Models for Extended
Batch Data" of Cowen et al. (2017) <doi:10.1111/biom.12701>.

%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}