%global __brp_check_rpaths %{nil}
%global packname  MOSS
%global packver   0.2.2
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.2.2
Release:          1%{?dist}%{?buildtag}
Summary:          Multi-Omic Integration via Sparse Singular Value Decomposition

License:          GPL-2
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-cluster 
BuildRequires:    R-CRAN-dbscan 
BuildRequires:    R-CRAN-Rtsne 
BuildRequires:    R-stats 
Requires:         R-CRAN-cluster 
Requires:         R-CRAN-dbscan 
Requires:         R-CRAN-Rtsne 
Requires:         R-stats 

%description
High dimensionality, noise and heterogeneity among samples and features
challenge the omic integration task. Here we present an omic integration
method based on sparse singular value decomposition (SVD) to deal with
these limitations, by: a. obtaining the main axes of variation of the
combined omics, b. imposing sparsity constraints at both subjects (rows)
and features (columns) levels using Elastic Net type of shrinkage, and c.
allowing both linear and non-linear projections (via t-Stochastic Neighbor
Embedding) of the omic data to detect clusters in very convoluted data
(Gonzalez-Reymundez et. al, 2022) <doi:10.1093/bioinformatics/btac179>.

%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}