%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  GEint
%global packver   1.1
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.1
Release:          1%{?dist}%{?buildtag}
Summary:          Misspecified Models for Gene-Environment Interaction

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


BuildRequires:    R-devel
Requires:         R-core
BuildArch:        noarch
BuildRequires:    R-CRAN-mvtnorm 
BuildRequires:    R-CRAN-bindata 
BuildRequires:    R-CRAN-nleqslv 
BuildRequires:    R-CRAN-pracma 
BuildRequires:    R-CRAN-speedglm 
BuildRequires:    R-CRAN-rje 
BuildRequires:    R-CRAN-geepack 
BuildRequires:    R-stats 
Requires:         R-CRAN-mvtnorm 
Requires:         R-CRAN-bindata 
Requires:         R-CRAN-nleqslv 
Requires:         R-CRAN-pracma 
Requires:         R-CRAN-speedglm 
Requires:         R-CRAN-rje 
Requires:         R-CRAN-geepack 
Requires:         R-stats 

%description
The first major functionality is to compute the bias in regression
coefficients of misspecified linear gene-environment interaction models.
The most generalized function for this objective is GE_bias(). However
GE_bias() requires specification of many higher order moments of
covariates in the model. If users are unsure about how to
calculate/estimate these higher order moments, it may be easier to use
GE_bias_normal_squaredmis(). This function places many more assumptions on
the covariates (most notably that they are all jointly generated from a
multivariate normal distribution) and is thus able to automatically
calculate many of the higher order moments automatically, necessitating
only that the user specify some covariances. There are also functions to
solve for the bias through simulation and non-linear equation solvers;
these can be used to check your work. Second major functionality is to
implement the Bootstrap Inference with Correct Sandwich (BICS) testing
procedure, which we have found to provide better finite-sample performance
than other inference procedures for testing GxE interaction. More details
on these functions are available in Sun, Carroll, Christiani, and Lin
(2018) <doi:10.1111/biom.12813>.

%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}