%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  PJFM
%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:          Variational Inference for High-Dimensional Joint Frailty Model

License:          GPL-2
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel >= 3.6.0
Requires:         R-core >= 3.6.0
BuildRequires:    R-CRAN-survival >= 3.2
BuildRequires:    R-CRAN-pracma >= 2.2
BuildRequires:    R-CRAN-statmod >= 1.4
BuildRequires:    R-CRAN-Matrix >= 1.3
BuildRequires:    R-CRAN-Rcpp >= 1.0.0
BuildRequires:    R-CRAN-RcppArmadillo 
BuildRequires:    R-CRAN-RcppEnsmallen 
Requires:         R-CRAN-survival >= 3.2
Requires:         R-CRAN-pracma >= 2.2
Requires:         R-CRAN-statmod >= 1.4
Requires:         R-CRAN-Matrix >= 1.3
Requires:         R-CRAN-Rcpp >= 1.0.0

%description
Joint frailty models have been widely used to study the associations
between recurrent events and a survival outcome. However, existing joint
frailty models only consider one or a few recurrent events and cannot deal
with high-dimensional recurrent events. This package can be used to fit
our recently developed penalized joint frailty model that can handle
high-dimensional recurrent events. Specifically, an adaptive lasso penalty
is imposed on the parameters for the effects of the recurrent events on
the survival outcome, which allows for variable selection. Also, our
algorithm is computationally efficient, which is based on the Gaussian
variational approximation method.

%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}