%global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname cloneRate %global packver 0.2.3 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} Version: 0.2.3 Release: 1%{?dist}%{?buildtag} Summary: Estimate Growth Rates from Phylogenetic Trees License: MIT + file LICENSE URL: https://cran.r-project.org/package=%{packname} Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz BuildRequires: R-devel >= 3.6.0 Requires: R-core >= 3.6.0 BuildRequires: R-CRAN-RcppParallel >= 5.0.1 BuildRequires: R-CRAN-ape >= 4.0 BuildRequires: R-CRAN-rstantools >= 2.3.1 BuildRequires: R-CRAN-rstan >= 2.18.1 BuildRequires: R-CRAN-StanHeaders >= 2.18.0 BuildRequires: R-CRAN-BH >= 1.66.0 BuildRequires: R-CRAN-Rmpfr >= 0.8 BuildRequires: R-CRAN-RcppEigen >= 0.3.3.3.0 BuildRequires: R-CRAN-Rcpp >= 0.12.0 BuildRequires: R-methods BuildRequires: R-CRAN-rstantools Requires: R-CRAN-ape >= 4.0 Requires: R-CRAN-rstantools >= 2.3.1 Requires: R-CRAN-rstan >= 2.18.1 Requires: R-CRAN-Rmpfr >= 0.8 Requires: R-CRAN-Rcpp >= 0.12.0 Requires: R-methods Requires: R-CRAN-rstantools %description Quickly estimate the net growth rate of a population or clone whose growth can be approximated by a birth-death branching process. Input should be phylogenetic tree(s) of clone(s) with edge lengths corresponding to either time or mutations. Based on coalescent results in Johnson et al. (2023) . Simulation techniques as well as growth rate methods build on prior work from Lambert A. (2018) and Stadler T. (2009) . %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}