%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  ulrb
%global packver   0.1.3
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.1.3
Release:          1%{?dist}%{?buildtag}
Summary:          Unsupervised Learning Based Definition of Microbial Rare Biosphere

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


BuildRequires:    R-devel >= 2.10
Requires:         R-core >= 2.10
BuildArch:        noarch
BuildRequires:    R-CRAN-cluster 
BuildRequires:    R-CRAN-dplyr 
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-CRAN-purrr 
BuildRequires:    R-CRAN-rlang 
BuildRequires:    R-stats 
BuildRequires:    R-CRAN-tidyr 
BuildRequires:    R-CRAN-clusterSim 
BuildRequires:    R-CRAN-gridExtra 
Requires:         R-CRAN-cluster 
Requires:         R-CRAN-dplyr 
Requires:         R-CRAN-ggplot2 
Requires:         R-CRAN-purrr 
Requires:         R-CRAN-rlang 
Requires:         R-stats 
Requires:         R-CRAN-tidyr 
Requires:         R-CRAN-clusterSim 
Requires:         R-CRAN-gridExtra 

%description
A tool to define rare biosphere. 'ulrb' solves the problem of the
definition of rarity by replacing human decision with an unsupervised
machine learning algorithm (partitioning around medoids, or k-medoids).
This algorithm works for any type of microbiome data, provided there is an
abundance score for each phylogenetic unit. For validation of this method
to several kinds of molecular data and environments, please see Pascoal et
al, 2023 (in preparation). Preliminary data suggest this method also works
well for non-microbiome data, if there is a species abundance table.

%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}