%global __brp_check_rpaths %{nil}
%global packname  PQLseq
%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:          Efficient Mixed Model Analysis of Count Data in Large-Scale Genomic Sequencing Studies

License:          GPL (>= 2)
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel >= 2.10
Requires:         R-core >= 2.10
BuildRequires:    R-CRAN-Rcpp >= 0.12.14
BuildRequires:    R-CRAN-foreach 
BuildRequires:    R-CRAN-doParallel 
BuildRequires:    R-parallel 
BuildRequires:    R-CRAN-Matrix 
BuildRequires:    R-methods 
BuildRequires:    R-CRAN-RcppArmadillo 
Requires:         R-CRAN-Rcpp >= 0.12.14
Requires:         R-CRAN-foreach 
Requires:         R-CRAN-doParallel 
Requires:         R-parallel 
Requires:         R-CRAN-Matrix 
Requires:         R-methods 

%description
An efficient tool designed for differential analysis of large-scale RNA
sequencing (RNAseq) data and Bisulfite sequencing (BSseq) data in the
presence of individual relatedness and population structure. 'PQLseq'
first fits a Generalized Linear Mixed Model (GLMM) with adjusted
covariates, predictor of interest and random effects to account for
population structure and individual relatedness, and then performs Wald
tests for each gene in RNAseq or site in BSseq.

%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
# 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}