%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  joineRML
%global packver   0.4.6
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.4.6
Release:          1%{?dist}%{?buildtag}
Summary:          Joint Modelling of Multivariate Longitudinal Data and Time-to-Event Outcomes

License:          GPL-3 | file LICENSE
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-lme4 >= 1.1.8
BuildRequires:    R-CRAN-Rcpp >= 0.12.7
BuildRequires:    R-CRAN-nlme 
BuildRequires:    R-CRAN-survival 
BuildRequires:    R-CRAN-cobs 
BuildRequires:    R-CRAN-doParallel 
BuildRequires:    R-CRAN-foreach 
BuildRequires:    R-CRAN-generics 
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-graphics 
BuildRequires:    R-CRAN-MASS 
BuildRequires:    R-CRAN-Matrix 
BuildRequires:    R-CRAN-mvtnorm 
BuildRequires:    R-parallel 
BuildRequires:    R-CRAN-randtoolbox 
BuildRequires:    R-stats 
BuildRequires:    R-CRAN-tibble 
BuildRequires:    R-utils 
BuildRequires:    R-CRAN-RcppArmadillo 
Requires:         R-CRAN-lme4 >= 1.1.8
Requires:         R-CRAN-Rcpp >= 0.12.7
Requires:         R-CRAN-nlme 
Requires:         R-CRAN-survival 
Requires:         R-CRAN-cobs 
Requires:         R-CRAN-doParallel 
Requires:         R-CRAN-foreach 
Requires:         R-CRAN-generics 
Requires:         R-CRAN-ggplot2 
Requires:         R-graphics 
Requires:         R-CRAN-MASS 
Requires:         R-CRAN-Matrix 
Requires:         R-CRAN-mvtnorm 
Requires:         R-parallel 
Requires:         R-CRAN-randtoolbox 
Requires:         R-stats 
Requires:         R-CRAN-tibble 
Requires:         R-utils 

%description
Fits the joint model proposed by Henderson and colleagues (2000)
<doi:10.1093/biostatistics/1.4.465>, but extended to the case of multiple
continuous longitudinal measures. The time-to-event data is modelled using
a Cox proportional hazards regression model with time-varying covariates.
The multiple longitudinal outcomes are modelled using a multivariate
version of the Laird and Ware linear mixed model. The association is
captured by a multivariate latent Gaussian process. The model is estimated
using a Monte Carlo Expectation Maximization algorithm. This project was
funded by the Medical Research Council (Grant number MR/M013227/1).

%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}