%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  pldamixture
%global packver   0.1.1
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.1.1
Release:          1%{?dist}%{?buildtag}
Summary:          Post-Linkage Data Analysis Based on Mixture Modelling

License:          GPL-2
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-stats 
BuildRequires:    R-CRAN-survival 
Requires:         R-stats 
Requires:         R-CRAN-survival 

%description
Perform inference in the secondary analysis setting with linked data
potentially containing mismatch errors. Only the linked data file may be
accessible and information about the record linkage process may be limited
or unavailable. Implements the 'General Framework for Regression with
Mismatched Data' developed by Slawski et al. (2023)
<doi:10.48550/arXiv.2306.00909>. The framework uses a mixture model for
pairs of linked records whose two components reflect distributions
conditional on match status, i.e., correct match or mismatch. Inference is
based on composite likelihood and the Expectation-Maximization (EM)
algorithm. The package currently supports Cox Proportional Hazards
Regression (right-censored data only) and Generalized Linear Regression
Models (Gaussian, Gamma, Poisson, and Logistic (binary models only)).
Information about the underlying record linkage process can be
incorporated into the method if available (e.g., assumed overall mismatch
rate, safe matches, predictors of match status, or predicted probabilities
of correct matches).

%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}