%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  LUCIDus
%global packver   3.0.1
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          3.0.1
Release:          1%{?dist}%{?buildtag}
Summary:          LUCID with Multiple Omics Data

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


BuildRequires:    R-devel >= 3.6.0
Requires:         R-core >= 3.6.0
BuildArch:        noarch
BuildRequires:    R-CRAN-mclust 
BuildRequires:    R-CRAN-nnet 
BuildRequires:    R-CRAN-boot 
BuildRequires:    R-CRAN-jsonlite 
BuildRequires:    R-CRAN-networkD3 
BuildRequires:    R-CRAN-progress 
BuildRequires:    R-stats 
BuildRequires:    R-utils 
BuildRequires:    R-CRAN-glasso 
BuildRequires:    R-CRAN-glmnet 
Requires:         R-CRAN-mclust 
Requires:         R-CRAN-nnet 
Requires:         R-CRAN-boot 
Requires:         R-CRAN-jsonlite 
Requires:         R-CRAN-networkD3 
Requires:         R-CRAN-progress 
Requires:         R-stats 
Requires:         R-utils 
Requires:         R-CRAN-glasso 
Requires:         R-CRAN-glmnet 

%description
An implementation of estimating the Latent Unknown Clusters By Integrating
Multi-omics Data (LUCID) model (Peng (2019)
<doi:10.1093/bioinformatics/btz667>). LUCID conducts integrated clustering
using exposures, omics data (and outcome as an option). This is a major
update from the last version while conserving all the previous features.
This package implements three different integration strategies for
multiple omics data analysis within the LUCID framework: LUCID early
integration (the original LUCID model), LUCID in parallel (intermediate),
and LUCID in serial (late). Automated model selection for each LUCID model
is available to obtain the optimal number of latent clusters, and an
integrated imputation approach is implemented to handle sporadic and
list-wise missing multiple omics data.

%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}