%global __brp_check_rpaths %{nil}
%global packname  vanquish
%global packver   1.0.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.0.0
Release:          3%{?dist}%{?buildtag}
Summary:          Variant Quality Investigation Helper

License:          GPL-2
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
BuildArch:        noarch
BuildRequires:    R-CRAN-changepoint 
BuildRequires:    R-CRAN-e1071 
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-stats 
BuildRequires:    R-CRAN-VGAM 
Requires:         R-CRAN-changepoint 
Requires:         R-CRAN-e1071 
Requires:         R-CRAN-ggplot2 
Requires:         R-stats 
Requires:         R-CRAN-VGAM 

%description
Imports Variant Calling Format file into R. It can detect whether a sample
contains contaminant from the same species. In the first stage of the
approach, a change-point detection method is used to identify copy number
variations for filtering. Next, features are extracted from the data for a
support vector machine model. For log-likelihood calculation, the
deviation parameter is estimated by maximum likelihood method. Using a
radial basis function kernel support vector machine, the contamination of
a sample can be detected.

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


%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

%files
%{rlibdir}/%{packname}