%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  rCNV
%global packver   1.3.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.3.0
Release:          1%{?dist}%{?buildtag}
Summary:          Detect Copy Number Variants from SNPs Data

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


BuildRequires:    R-devel >= 3.6.0
Requires:         R-core >= 3.6.0
BuildArch:        noarch
BuildRequires:    R-CRAN-data.table 
BuildRequires:    R-graphics 
BuildRequires:    R-CRAN-colorspace 
BuildRequires:    R-CRAN-R.utils 
BuildRequires:    R-CRAN-qgraph 
BuildRequires:    R-CRAN-stringr 
Requires:         R-CRAN-data.table 
Requires:         R-graphics 
Requires:         R-CRAN-colorspace 
Requires:         R-CRAN-R.utils 
Requires:         R-CRAN-qgraph 
Requires:         R-CRAN-stringr 

%description
Functions in this package will import filtered variant call format (VCF)
files of SNPs data and generate data sets to detect copy number variants,
visualize them and do downstream analyses with copy number variants(e.g.
Environmental association analyses).

%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}