%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  rPBK
%global packver   0.2.4
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.2.4
Release:          1%{?dist}%{?buildtag}
Summary:          Inference and Prediction of Generic Physiologically-Based Kinetic Models

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


BuildRequires:    R-devel >= 3.4.0
Requires:         R-core >= 3.4.0
BuildRequires:    R-CRAN-RcppParallel >= 5.0.1
BuildRequires:    R-CRAN-rstan >= 2.26.0
BuildRequires:    R-CRAN-StanHeaders >= 2.26.0
BuildRequires:    R-CRAN-BH >= 1.66.0
BuildRequires:    R-CRAN-RcppEigen >= 0.3.3.3.0
BuildRequires:    R-CRAN-Rcpp >= 0.12.0
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-methods 
BuildRequires:    R-CRAN-rstantools 
BuildRequires:    R-CRAN-rstantools
Requires:         R-CRAN-rstan >= 2.26.0
Requires:         R-CRAN-Rcpp >= 0.12.0
Requires:         R-CRAN-ggplot2 
Requires:         R-methods 
Requires:         R-CRAN-rstantools 
Requires:         R-CRAN-rstantools

%description
Fit and simulate any kind of physiologically-based kinetic ('PBK') models
whatever the number of compartments. Moreover, it allows to account for
any link between pairs of compartments, as well as any link of each of the
compartments with the external medium. Such generic PBK models have today
applications in pharmacology (PBPK models) to describe drug effects, in
toxicology and ecotoxicology (PBTK models) to describe chemical substance
effects. In case of exposure to a parent compound (drug or chemical) the
'rPBK' package allows to consider metabolites, whatever their number and
their phase (I, II, ...). Last but not least, package 'rPBK' can also be
used for dynamic flux balance analysis (dFBA) to deal with metabolic
networks. See also Charles et al. (2022) <doi:10.1101/2022.04.29.490045>.

%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}