%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  DEHOGT
%global packver   0.99.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.99.0
Release:          1%{?dist}%{?buildtag}
Summary:          Differentially Expressed Heterogeneous Overdispersion Gene Test for Count Data

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-CRAN-foreach 
BuildRequires:    R-CRAN-MASS 
Requires:         R-CRAN-doParallel 
Requires:         R-CRAN-foreach 
Requires:         R-CRAN-MASS 

%description
Implements a generalized linear model approach for detecting
differentially expressed genes across treatment groups in count data. The
package supports both quasi-Poisson and negative binomial models to handle
over-dispersion, ensuring robust identification of differential
expression. It allows for the inclusion of treatment effects and gene-wise
covariates, as well as normalization factors for accurate scaling across
samples. Additionally, it incorporates statistical significance testing
with options for p-value adjustment and log2 fold range thresholds, making
it suitable for RNA-seq analysis as described in by Xu et al., (2024)
<doi:10.1371/journal.pone.0300565>.

%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}