%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  CDGHMM
%global packver   0.1.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.1.0
Release:          1%{?dist}%{?buildtag}
Summary:          Hidden Markov Models for Multivariate Panel Data

License:          GPL (>= 2)
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-MASS 
BuildRequires:    R-CRAN-mvtnorm 
BuildRequires:    R-CRAN-ramify 
BuildRequires:    R-CRAN-cluster 
Requires:         R-CRAN-MASS 
Requires:         R-CRAN-mvtnorm 
Requires:         R-CRAN-ramify 
Requires:         R-CRAN-cluster 

%description
Estimates hidden Markov models from the family of Cholesky-decomposed
Gaussian hidden Markov models (CDGHMM) under various missingness schemes.
This family improves upon estimation of traditional Gaussian HMMs by
directly modelling the distinct correlation structures that arise from
longitudinal data, as well as, controlling for dropped out observations
and non-random missingness. See Neal, Sochaniwsky and McNicholas (2024)
<DOI:10.48550/arXiv.2404.04122>.

%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}