%global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname EpiPvr %global packver 0.0.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} Version: 0.0.1 Release: 1%{?dist}%{?buildtag} Summary: Estimating Plant Pathogen Epidemiology Parameters from Laboratory Assays License: GPL-3 URL: https://cran.r-project.org/package=%{packname} Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz BuildRequires: R-devel >= 3.5 Requires: R-core >= 3.5 BuildRequires: R-CRAN-RcppParallel >= 5.0.1 BuildRequires: R-CRAN-rstantools >= 2.5.0 BuildRequires: R-CRAN-rstan >= 2.18.1 BuildRequires: R-CRAN-StanHeaders >= 2.18.0 BuildRequires: R-CRAN-BH >= 1.66.0 BuildRequires: R-CRAN-RcppEigen >= 0.3.3.3.0 BuildRequires: R-CRAN-Rcpp >= 0.12.0 BuildRequires: R-methods BuildRequires: R-stats BuildRequires: R-CRAN-posterior BuildRequires: R-CRAN-rstantools Requires: R-CRAN-RcppParallel >= 5.0.1 Requires: R-CRAN-rstantools >= 2.5.0 Requires: R-CRAN-rstan >= 2.18.1 Requires: R-CRAN-Rcpp >= 0.12.0 Requires: R-methods Requires: R-stats Requires: R-CRAN-posterior Requires: R-CRAN-rstantools %description Provides functions for estimating plant pathogen parameters from access period (AP) experiments. Separate functions are implemented for semi-persistently transmitted (SPT) and persistently transmitted (PT) pathogens. The common AP experiment exposes insect cohorts to infected source plants, healthy test plants, and intermediate plants (for PT pathogens). The package allows estimation of acquisition and inoculation rates during feeding, recovery rates, and latent progression rates (for PT pathogens). Additional functions support inference of epidemic risk from pathogen and local parameters, and also simulate AP experiment data. The functions implement probability models for epidemiological analysis, as derived in Donnelly et al. (2025), . These models were originally implemented in the 'EpiPv' 'GitHub' package. %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}