%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  rbiom
%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:          Read/Write, Transform, and Summarize 'BIOM' Data

License:          AGPL-3
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
BuildRequires:    R-CRAN-magrittr 
BuildRequires:    R-methods 
BuildRequires:    R-CRAN-plyr 
BuildRequires:    R-CRAN-Rcpp 
BuildRequires:    R-CRAN-RcppParallel 
BuildRequires:    R-CRAN-rjson 
BuildRequires:    R-CRAN-rlang 
BuildRequires:    R-CRAN-R.utils 
BuildRequires:    R-CRAN-slam 
BuildRequires:    R-CRAN-openxlsx 
Requires:         R-CRAN-magrittr 
Requires:         R-methods 
Requires:         R-CRAN-plyr 
Requires:         R-CRAN-Rcpp 
Requires:         R-CRAN-RcppParallel 
Requires:         R-CRAN-rjson 
Requires:         R-CRAN-rlang 
Requires:         R-CRAN-R.utils 
Requires:         R-CRAN-slam 
Requires:         R-CRAN-openxlsx 

%description
A toolkit for working with Biological Observation Matrix ('BIOM') files.
Features include reading/writing all 'BIOM' formats, rarefaction, alpha
diversity, beta diversity (including 'UniFrac'), summarizing counts by
taxonomic level, and sample subsetting. Standalone functions for reading,
writing, and subsetting phylogenetic trees are also provided. All CPU
intensive operations are encoded in C with multi-thread support.

%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}