%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  MEDseq
%global packver   1.4.1
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.4.1
Release:          1%{?dist}%{?buildtag}
Summary:          Mixtures of Exponential-Distance Models with Covariates

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


BuildRequires:    R-devel >= 4.0.0
Requires:         R-core >= 4.0.0
BuildArch:        noarch
BuildRequires:    R-CRAN-nnet >= 7.3.0
BuildRequires:    R-CRAN-TraMineR >= 1.6
BuildRequires:    R-CRAN-matrixStats >= 1.0.0
BuildRequires:    R-CRAN-cluster 
BuildRequires:    R-CRAN-seriation 
BuildRequires:    R-CRAN-stringdist 
BuildRequires:    R-CRAN-WeightedCluster 
Requires:         R-CRAN-nnet >= 7.3.0
Requires:         R-CRAN-TraMineR >= 1.6
Requires:         R-CRAN-matrixStats >= 1.0.0
Requires:         R-CRAN-cluster 
Requires:         R-CRAN-seriation 
Requires:         R-CRAN-stringdist 
Requires:         R-CRAN-WeightedCluster 

%description
Implements a model-based clustering method for categorical life-course
sequences relying on mixtures of exponential-distance models introduced by
Murphy et al. (2021) <doi:10.1111/rssa.12712>. A range of flexible
precision parameter settings corresponding to weighted generalisations of
the Hamming distance metric are considered, along with the potential
inclusion of a noise component. Gating covariates can be supplied in order
to relate sequences to baseline characteristics and sampling weights are
also accommodated. The models are fitted using the EM algorithm and tools
for visualising the results are also provided.

%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}