%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  prepR4pcm
%global packver   1.0.3
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.0.3
Release:          1%{?dist}%{?buildtag}
Summary:          Prepare Data and Trees for Phylogenetic Comparative Methods

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


BuildRequires:    R-devel >= 4.1.0
Requires:         R-core >= 4.1.0
BuildArch:        noarch
BuildRequires:    R-CRAN-ape 
BuildRequires:    R-CRAN-cli 
BuildRequires:    R-CRAN-rlang 
BuildRequires:    R-CRAN-tibble 
Requires:         R-CRAN-ape 
Requires:         R-CRAN-cli 
Requires:         R-CRAN-rlang 
Requires:         R-CRAN-tibble 

%description
Reconcile species names across datasets and phylogenetic trees for
comparative biology workflows. Identifies mismatches due to formatting
differences, taxonomic synonymy, and spelling errors. Produces detailed
reports documenting how each name was resolved, which taxonomic authority
was used, and what remains unresolved. Supports exact matching, name
normalisation, synonym resolution via local taxonomic databases, and fuzzy
matching for likely typos. Detects taxonomic splits and lumps. For
methodological context, see Nakagawa et al. (2026) <doi:10.32942/X2468Z>.

%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}