%global __brp_check_rpaths %{nil}
%global packname  adjSURVCI
%global packver   1.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.0
Release:          1%{?dist}%{?buildtag}
Summary:          Parameter and Adjusted Probability Estimation for Right-Censored Data

License:          GPL (>= 2)
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel
Requires:         R-core
BuildRequires:    R-CRAN-Rcpp >= 1.0.7
BuildRequires:    R-CRAN-survival 
BuildRequires:    R-CRAN-RcppArmadillo 
Requires:         R-CRAN-Rcpp >= 1.0.7
Requires:         R-CRAN-survival 

%description
Functions in this package fit a stratified Cox proportional hazards and a
proportional subdistribution hazards model by extending Zhang et al.,
(2007) <doi: 10.1016/j.cmpb.2007.07.010> and Zhang et al., (2011) <doi:
10.1016/j.cmpb.2010.07.005> respectively to clustered right-censored data.
The functions also provide the estimates of the cumulative baseline hazard
along with their standard errors. Furthermore, the adjusted survival and
cumulative incidence probabilities are also provided along with their
standard errors. Finally, the estimate of cumulative incidence and
survival probabilities given a vector of covariates along with their
standard errors are also provided.

%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}