%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  nbTransmission
%global packver   1.1.4
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.1.4
Release:          1%{?dist}%{?buildtag}
Summary:          Naive Bayes Transmission Analysis

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


BuildRequires:    R-devel >= 3.4.0
Requires:         R-core >= 3.4.0
BuildArch:        noarch
BuildRequires:    R-CRAN-dplyr 
BuildRequires:    R-CRAN-rlang 
BuildRequires:    R-CRAN-caret 
BuildRequires:    R-CRAN-lubridate 
BuildRequires:    R-CRAN-poisbinom 
BuildRequires:    R-stats 
BuildRequires:    R-CRAN-tidyr 
BuildRequires:    R-utils 
Requires:         R-CRAN-dplyr 
Requires:         R-CRAN-rlang 
Requires:         R-CRAN-caret 
Requires:         R-CRAN-lubridate 
Requires:         R-CRAN-poisbinom 
Requires:         R-stats 
Requires:         R-CRAN-tidyr 
Requires:         R-utils 

%description
Estimates the relative transmission probabilities between cases in an
infectious disease outbreak or cluster using naive Bayes. Included are
various functions to use these probabilities to estimate transmission
parameters such as the generation/serial interval and reproductive number
as well as finding the contribution of covariates to the probabilities and
visualizing results. The ideal use is for an infectious disease dataset
with metadata on the majority of cases but more informative data such as
contact tracing or pathogen whole genome sequencing on only a subset of
cases. For a detailed description of the methods see Leavitt et al. (2020)
<doi:10.1093/ije/dyaa031>.

%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}