%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  maxaltall
%global packver   0.1.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.1.0
Release:          1%{?dist}%{?buildtag}
Summary:          'FASTA' ML and ‘altall’ Sequences from IQ-TREE .state Files

License:          GPL (>= 3)
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel
Requires:         R-core
BuildArch:        noarch
BuildRequires:    R-CRAN-data.table 
BuildRequires:    R-CRAN-dplyr 
BuildRequires:    R-CRAN-magrittr 
BuildRequires:    R-CRAN-tidyr 
Requires:         R-CRAN-data.table 
Requires:         R-CRAN-dplyr 
Requires:         R-CRAN-magrittr 
Requires:         R-CRAN-tidyr 

%description
Takes a .state file generated by IQ-TREE as an input and, for each
ancestral node present in the file, generates a FASTA-formatted maximum
likelihood (ML) sequence as well as an ‘AltAll’ sequence in which
uncertain sites, determined by the two parameters thres_1 and thres_2,
have the maximum likelihood state swapped with the next most likely state
as described in Geeta N. Eick, Jamie T. Bridgham, Douglas P. Anderson,
Michael J. Harms, and Joseph W. Thornton (2017), "Robustness of
Reconstructed Ancestral Protein Functions to Statistical Uncertainty"
<doi:10.1093/molbev/msw223>.

%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}