%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  fastFGEE
%global packver   0.2.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.2.0
Release:          1%{?dist}%{?buildtag}
Summary:          Fast Functional Generalized Estimating Equations via a One-Step Estimator

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


BuildRequires:    R-devel >= 4.2
Requires:         R-core >= 4.2
BuildRequires:    R-CRAN-refund >= 0.1.40
BuildRequires:    R-CRAN-data.table 
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-CRAN-gridExtra 
BuildRequires:    R-CRAN-MASS 
BuildRequires:    R-CRAN-Matrix 
BuildRequires:    R-CRAN-mgcv 
BuildRequires:    R-CRAN-Rcpp 
Requires:         R-CRAN-refund >= 0.1.40
Requires:         R-CRAN-data.table 
Requires:         R-CRAN-ggplot2 
Requires:         R-CRAN-gridExtra 
Requires:         R-CRAN-MASS 
Requires:         R-CRAN-Matrix 
Requires:         R-CRAN-mgcv 
Requires:         R-CRAN-Rcpp 

%description
Fits functional generalized estimating equations for longitudinal
functional outcomes and covariates using a one-step estimator that is fast
even for large cluster sizes or large numbers of clusters. The package
supports quasi-likelihoods derived from a range of distributions, with
substantial simulations run for quasi-likelihoods derived from Gaussian,
binomial, Poisson, negative binomial, Gamma and beta families. It supports
common link functions and several working correlation structures. An
optimized engine constructs cluster score and sensitivity statistics in
one pass, provides coefficient-space Gaussian cross-validation,
analytic-gradient fast cluster cross-validation, and an experimental
sandwich-scaled working restricted quasi-likelihood selector. Internal
compiled routines provide symmetric positive-definite Cholesky solves and
exact tridiagonal precision operations for irregularly sampled
continuous-time AR(1) working correlations. Uncertainty quantification is
based on sandwich variance estimators and studentized wild cluster
bootstrap procedures for cluster-robust pointwise intervals and optional
simultaneous bands. The package implements methods described in Loewinger
et al. (2025) <https://pmc.ncbi.nlm.nih.gov/articles/PMC12306803/>.

%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}