%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  BuyseTest
%global packver   2.4.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          2.4.0
Release:          1%{?dist}%{?buildtag}
Summary:          Generalized Pairwise Comparisons

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


BuildRequires:    R-devel >= 2.10
Requires:         R-core >= 2.10
BuildRequires:    R-CRAN-Rcpp 
BuildRequires:    R-CRAN-data.table 
BuildRequires:    R-CRAN-doParallel 
BuildRequires:    R-CRAN-foreach 
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-methods 
BuildRequires:    R-CRAN-lava 
BuildRequires:    R-parallel 
BuildRequires:    R-CRAN-prodlim 
BuildRequires:    R-CRAN-riskRegression 
BuildRequires:    R-CRAN-rlang 
BuildRequires:    R-stats 
BuildRequires:    R-stats4 
BuildRequires:    R-utils 
BuildRequires:    R-CRAN-RcppArmadillo 
Requires:         R-CRAN-Rcpp 
Requires:         R-CRAN-data.table 
Requires:         R-CRAN-doParallel 
Requires:         R-CRAN-foreach 
Requires:         R-CRAN-ggplot2 
Requires:         R-methods 
Requires:         R-CRAN-lava 
Requires:         R-parallel 
Requires:         R-CRAN-prodlim 
Requires:         R-CRAN-riskRegression 
Requires:         R-CRAN-rlang 
Requires:         R-stats 
Requires:         R-stats4 
Requires:         R-utils 

%description
Implementation of the Generalized Pairwise Comparisons (GPC) as defined in
Buyse (2010) <doi:10.1002/sim.3923> for complete observations, and
extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with
right-censoring. GPC compare two groups of observations (intervention vs.
control group) regarding several prioritized endpoints to estimate the
probability that a random observation drawn from one group performs better
than a random observation drawn from the other group (Mann-Whitney
parameter). The net benefit and win ratio statistics, i.e. the difference
and ratio between the probabilities relative to the intervention and
control groups, can then also be estimated. Confidence intervals and
p-values are obtained based on asymptotic results (Ozenne 2021
<doi:10.1177/09622802211037067>), non-parametric bootstrap, or
permutations. The software enables the use of thresholds of minimal
importance difference, stratification, non-prioritized endpoints (O Brien
test), and can handle right-censoring and competing-risks.

%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}