%global __brp_check_rpaths %{nil}
%global packname  PheCAP
%global packver   1.2.1
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.2.1
Release:          1%{?dist}%{?buildtag}
Summary:          High-Throughput Phenotyping with EHR using a Common Automated Pipeline

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


BuildRequires:    R-devel >= 3.3.0
Requires:         R-core >= 3.3.0
BuildArch:        noarch
BuildRequires:    R-graphics 
BuildRequires:    R-methods 
BuildRequires:    R-stats 
BuildRequires:    R-utils 
BuildRequires:    R-CRAN-glmnet 
BuildRequires:    R-CRAN-RMySQL 
Requires:         R-graphics 
Requires:         R-methods 
Requires:         R-stats 
Requires:         R-utils 
Requires:         R-CRAN-glmnet 
Requires:         R-CRAN-RMySQL 

%description
Implement surrogate-assisted feature extraction (SAFE) and common machine
learning approaches to train and validate phenotyping models. Background
and details about the methods can be found at Zhang et al. (2019)
<doi:10.1038/s41596-019-0227-6>, Yu et al. (2017)
<doi:10.1093/jamia/ocw135>, and Liao et al. (2015)
<doi:10.1136/bmj.h1885>.

%prep
%setup -q -c -n %{packname}

find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \;
[ -d %{packname}/src ] && find %{packname}/src -type f -exec \
  sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true

%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
find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \;

%files
%{rlibdir}/%{packname}