%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  phylepic
%global packver   0.3.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.3.0
Release:          1%{?dist}%{?buildtag}
Summary:          Combined Visualisation of Phylogenetic and Epidemiological Data

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


BuildRequires:    R-devel >= 4.1
Requires:         R-core >= 4.1
BuildArch:        noarch
BuildRequires:    R-CRAN-ggplot2 >= 4.0.0
BuildRequires:    R-CRAN-ape 
BuildRequires:    R-CRAN-cli 
BuildRequires:    R-CRAN-cowplot 
BuildRequires:    R-CRAN-dplyr 
BuildRequires:    R-CRAN-forcats 
BuildRequires:    R-CRAN-ggnewscale 
BuildRequires:    R-CRAN-ggraph 
BuildRequires:    R-CRAN-igraph 
BuildRequires:    R-CRAN-lifecycle 
BuildRequires:    R-CRAN-rlang 
BuildRequires:    R-CRAN-scales 
BuildRequires:    R-CRAN-tidygraph 
Requires:         R-CRAN-ggplot2 >= 4.0.0
Requires:         R-CRAN-ape 
Requires:         R-CRAN-cli 
Requires:         R-CRAN-cowplot 
Requires:         R-CRAN-dplyr 
Requires:         R-CRAN-forcats 
Requires:         R-CRAN-ggnewscale 
Requires:         R-CRAN-ggraph 
Requires:         R-CRAN-igraph 
Requires:         R-CRAN-lifecycle 
Requires:         R-CRAN-rlang 
Requires:         R-CRAN-scales 
Requires:         R-CRAN-tidygraph 

%description
A collection of utilities and 'ggplot2' extensions to assist with
visualisations in genomic epidemiology. This includes the 'phylepic'
chart, a visual combination of a phylogenetic tree and a matched epidemic
curve. The included 'ggplot2' extensions such as date axes binned by week
are relevant for other applications in epidemiology and beyond. The
approach is described in Suster et al. (2024)
<doi:10.1101/2024.04.02.24305229>.

%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}