%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname LTFHPlus
%global packver 2.1.1
%global rlibdir /usr/local/lib/R/library
Name: R-CRAN-%{packname}
Version: 2.1.1
Release: 1%{?dist}%{?buildtag}
Summary: Implementation of LT-FH++
License: GPL-3
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-batchmeans
BuildRequires: R-CRAN-dplyr
BuildRequires: R-CRAN-future.apply
BuildRequires: R-CRAN-future
BuildRequires: R-CRAN-purrr
BuildRequires: R-CRAN-Rcpp
BuildRequires: R-CRAN-rlang
BuildRequires: R-stats
BuildRequires: R-CRAN-stringr
BuildRequires: R-CRAN-tibble
BuildRequires: R-CRAN-tmvtnorm
BuildRequires: R-CRAN-tidyselect
BuildRequires: R-CRAN-igraph
BuildRequires: R-CRAN-xgboost
BuildRequires: R-CRAN-tidyr
Requires: R-CRAN-batchmeans
Requires: R-CRAN-dplyr
Requires: R-CRAN-future.apply
Requires: R-CRAN-future
Requires: R-CRAN-purrr
Requires: R-CRAN-Rcpp
Requires: R-CRAN-rlang
Requires: R-stats
Requires: R-CRAN-stringr
Requires: R-CRAN-tibble
Requires: R-CRAN-tmvtnorm
Requires: R-CRAN-tidyselect
Requires: R-CRAN-igraph
Requires: R-CRAN-xgboost
Requires: R-CRAN-tidyr
%description
Implementation of LT-FH++, an extension of the liability threshold family
history (LT-FH) model. LT-FH++ uses a Gibbs sampler for sampling from the
truncated multivariate normal distribution and allows for flexible family
structures. LT-FH++ was first described in Pedersen, Emil M., et al.
(2022) as an
extension to LT-FH with more flexible family structures, and again as the
age-dependent liability threshold (ADuLT) model Pedersen, Emil M., et al.
(2023) as an
alternative to traditional time-to-event genome-wide association studies,
where family history was not considered.
%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}