%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  cyclomort
%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:          Survival Modeling with a Periodic Hazard Function

License:          GPL (>= 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
BuildArch:        noarch
BuildRequires:    R-CRAN-flexsurv 
BuildRequires:    R-CRAN-lubridate 
BuildRequires:    R-CRAN-magrittr 
BuildRequires:    R-CRAN-mvtnorm 
BuildRequires:    R-CRAN-plyr 
BuildRequires:    R-CRAN-scales 
BuildRequires:    R-stats 
BuildRequires:    R-CRAN-survival 
Requires:         R-CRAN-flexsurv 
Requires:         R-CRAN-lubridate 
Requires:         R-CRAN-magrittr 
Requires:         R-CRAN-mvtnorm 
Requires:         R-CRAN-plyr 
Requires:         R-CRAN-scales 
Requires:         R-stats 
Requires:         R-CRAN-survival 

%description
Modeling periodic mortality (or other time-to event) processes from
right-censored data. Given observations of a process with a known period
(e.g. 365 days, 24 hours), functions determine the number, intensity,
timing, and duration of peaks of periods of elevated hazard within a
period.  The underlying model is a mixed wrapped Cauchy function fitted
using maximum likelihoods (details in Gurarie et al. (2020)
<doi:10.1111/2041-210X.13305>). The development of these tools was
motivated by the strongly seasonal mortality patterns observed in many
wild animal populations. Thus, the respective periods of higher mortality
can be identified as "mortality seasons".

%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}