%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  gateR
%global packver   0.1.15
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.1.15
Release:          1%{?dist}%{?buildtag}
Summary:          Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation

License:          Apache License (>= 2.0)
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-CRAN-fields 
BuildRequires:    R-graphics 
BuildRequires:    R-grDevices 
BuildRequires:    R-CRAN-lifecycle 
BuildRequires:    R-CRAN-rlang 
BuildRequires:    R-CRAN-sparr 
BuildRequires:    R-CRAN-SpatialPack 
BuildRequires:    R-CRAN-spatstat.geom 
BuildRequires:    R-stats 
BuildRequires:    R-CRAN-terra 
BuildRequires:    R-CRAN-tibble 
Requires:         R-CRAN-fields 
Requires:         R-graphics 
Requires:         R-grDevices 
Requires:         R-CRAN-lifecycle 
Requires:         R-CRAN-rlang 
Requires:         R-CRAN-sparr 
Requires:         R-CRAN-SpatialPack 
Requires:         R-CRAN-spatstat.geom 
Requires:         R-stats 
Requires:         R-CRAN-terra 
Requires:         R-CRAN-tibble 

%description
Estimates statistically significant marker combination values within which
one immunologically distinctive group (i.e., disease case) is more
associated than another group (i.e., healthy control), successively, using
various combinations (i.e., "gates") of markers to examine features of
cells that may be different between groups. For a two-group comparison,
the 'gateR' package uses the spatial relative risk function estimated
using the 'sparr' package. Details about the 'sparr' package methods can
be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>.
Details about kernel density estimation can be found in J. F. Bithell
(1990) <doi:10.1002/sim.4780090616>. More information about relative risk
functions using kernel density estimation can be found in J. F. Bithell
(1991) <doi:10.1002/sim.4780101112>.

%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}