%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  RCNA
%global packver   1.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.0
Release:          1%{?dist}%{?buildtag}
Summary:          Robust Copy Number Alteration Detection (RCNA)

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


BuildRequires:    R-devel >= 3.5.0
Requires:         R-core >= 3.5.0
BuildArch:        noarch
BuildRequires:    R-CRAN-doParallel 
BuildRequires:    R-methods 
BuildRequires:    R-utils 
BuildRequires:    R-CRAN-modeest 
BuildRequires:    R-CRAN-data.table 
BuildRequires:    R-CRAN-foreach 
BuildRequires:    R-CRAN-R.utils 
Requires:         R-CRAN-doParallel 
Requires:         R-methods 
Requires:         R-utils 
Requires:         R-CRAN-modeest 
Requires:         R-CRAN-data.table 
Requires:         R-CRAN-foreach 
Requires:         R-CRAN-R.utils 

%description
Detects copy number alteration events in targeted exon sequencing data for
tumor samples without matched normal controls. The advantage of this
method is that it can be applied to smaller sequencing panels including
evaluations of exon, transcript, gene, or even user specified genetic
regions of interest. Functions in the package include steps for GC-content
correction, calculation of quantile based normal karyotype ranges, and
calculation of feature score.  Cutoffs for "normal" quantile and score are
user-adjustable.

%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}