%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  demulticoder
%global packver   0.1.2
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.1.2
Release:          1%{?dist}%{?buildtag}
Summary:          Simultaneous Analysis of Multiplexed Metabarcodes

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


BuildRequires:    R-devel >= 3.0.2
Requires:         R-core >= 3.0.2
BuildArch:        noarch
BuildRequires:    R-CRAN-furrr 
BuildRequires:    R-CRAN-purrr 
BuildRequires:    R-CRAN-readr 
BuildRequires:    R-CRAN-stringr 
BuildRequires:    R-CRAN-tidyr 
BuildRequires:    R-CRAN-dplyr 
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-CRAN-tibble 
BuildRequires:    R-utils 
Requires:         R-CRAN-furrr 
Requires:         R-CRAN-purrr 
Requires:         R-CRAN-readr 
Requires:         R-CRAN-stringr 
Requires:         R-CRAN-tidyr 
Requires:         R-CRAN-dplyr 
Requires:         R-CRAN-ggplot2 
Requires:         R-CRAN-tibble 
Requires:         R-utils 

%description
A comprehensive set of wrapper functions for the analysis of multiplex
metabarcode data. It includes robust wrappers for 'Cutadapt' and 'DADA2'
to trim primers, filter reads, perform amplicon sequence variant (ASV)
inference, and assign taxonomy. The package can handle single metabarcode
datasets, datasets with two pooled metabarcodes, or multiple datasets
simultaneously. The final output is a matrix per metabarcode, containing
both ASV abundance data and associated taxonomic assignments. An optional
function converts these matrices into 'phyloseq' and 'taxmap' objects. For
more information on 'DADA2', including information on how DADA2 infers
samples sequences, see Callahan et al. (2016) <doi:10.1038/nmeth.3869>.
For more details on the demulticoder R package see Sudermann et al. (2025)
<doi:10.1094/PHYTO-02-25-0043-FI>.

%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}