%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  rtestim
%global packver   1.0.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.0.0
Release:          1%{?dist}%{?buildtag}
Summary:          Estimate the Effective Reproductive Number with Trend Filtering

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


BuildRequires:    R-devel >= 3.6.2
Requires:         R-core >= 3.6.2
BuildRequires:    R-CRAN-checkmate 
BuildRequires:    R-CRAN-cli 
BuildRequires:    R-CRAN-dspline 
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-CRAN-Matrix 
BuildRequires:    R-methods 
BuildRequires:    R-CRAN-Rcpp 
BuildRequires:    R-CRAN-rlang 
BuildRequires:    R-CRAN-tibble 
BuildRequires:    R-CRAN-tvdenoising 
BuildRequires:    R-CRAN-vctrs 
BuildRequires:    R-CRAN-BH 
BuildRequires:    R-CRAN-RcppEigen 
BuildRequires:    R-CRAN-testthat 
Requires:         R-CRAN-checkmate 
Requires:         R-CRAN-cli 
Requires:         R-CRAN-dspline 
Requires:         R-CRAN-ggplot2 
Requires:         R-CRAN-Matrix 
Requires:         R-methods 
Requires:         R-CRAN-Rcpp 
Requires:         R-CRAN-rlang 
Requires:         R-CRAN-tibble 
Requires:         R-CRAN-tvdenoising 
Requires:         R-CRAN-vctrs 

%description
Use trend filtering, a type of regularized nonparametric regression, to
estimate the instantaneous reproduction number, also called Rt. This value
roughly says how many new infections will result from each new infection
today.  Values larger than 1 indicate that an epidemic is growing while
those less than 1 indicate decline. For more details about this
methodology, see Liu, Cai, Gustafson, and McDonald (2024)
<doi:10.1371/journal.pcbi.1012324>.

%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}