%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  BSET
%global packver   1.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.0
Release:          1%{?dist}%{?buildtag}
Summary:          A Bayesian Surrogate Evaluation Test

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


BuildRequires:    R-devel >= 3.5
Requires:         R-core >= 3.5
BuildArch:        noarch
BuildRequires:    R-CRAN-rstan 
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-CRAN-future 
BuildRequires:    R-parallel 
BuildRequires:    R-CRAN-mvtnorm 
BuildRequires:    R-CRAN-dplyr 
BuildRequires:    R-CRAN-SurrogateRank 
BuildRequires:    R-CRAN-Rdpack 
BuildRequires:    R-CRAN-rlang 
BuildRequires:    R-CRAN-rstantools
Requires:         R-CRAN-rstan 
Requires:         R-CRAN-ggplot2 
Requires:         R-CRAN-future 
Requires:         R-parallel 
Requires:         R-CRAN-mvtnorm 
Requires:         R-CRAN-dplyr 
Requires:         R-CRAN-SurrogateRank 
Requires:         R-CRAN-Rdpack 
Requires:         R-CRAN-rlang 
Requires:         R-CRAN-rstantools

%description
An implementation of the Bayesian Surrogate Evaluation Test (BSET) for
assessing the validity of surrogate markers in clinical trials. Provides
hypothesis testing tools to evaluate whether a surrogate can reliably
estimate the causal effect of a treatment on a primary outcome. Implements
the imputation-based Bayesian methodology of Carlotti and Parast (2026)
<doi:10.48550/arXiv.2603.14381>, extending the frequentist rank-based
approach of Parast et al. (2024) <doi:10.1093/biomtc/ujad035>. Addresses
key limitations of the frequentist method, including the lack of causal
interpretability and the inability to adjust for covariates in the
estimation process.

%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}