File R-glmmPen.spec of Package R-glmmPen
# Automatically generated by CRAN2OBS
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# Spec file for package glmmPen
# This file is auto-generated using information in the package source,
# esp. Description and Summary. Improvements in that area should be
# discussed with upstream.
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%global packname glmmPen
%global rlibdir %{_libdir}/R/library
Name: R-%{packname}
Version: 1.5.4.8
Release: 0
Summary: High Dimensional Penalized Generalized Linear Mixed Models (pGLMM)
Group: Development/Libraries/Other
License: GPL (>= 2)
URL: http://cran.r-project.org/web/packages/%{packname}
Source: glmmPen_1.5.4.8.tar.gz
Requires: R-base
Requires: R-lme4
Requires: R-bigmemory
Requires: R-Rcpp
Requires: R-ggplot2
Requires: R-ncvreg
Requires: R-reshape2
Requires: R-rstan
Requires: R-stringr
Requires: R-mvtnorm
Requires: R-rstantools
Requires: R-RcppParallel
Requires: R-BH
Requires: R-RcppArmadillo
Requires: R-RcppEigen
Requires: R-StanHeaders
Requires: R-bigmemory.sri
Requires: R-uuid
Requires: R-cli
Requires: R-gtable
Requires: R-isoband
Requires: R-lifecycle
Requires: R-rlang
Requires: R-S7
Requires: R-scales
Requires: R-vctrs
Requires: R-withr
Requires: R-minqa
Requires: R-nloptr
Requires: R-reformulas
Requires: R-plyr
Requires: R-inline
Requires: R-gridExtra
Requires: R-loo
Requires: R-pkgbuild
Requires: R-QuickJSR
Requires: R-desc
Requires: R-glue
Requires: R-magrittr
Requires: R-stringi
Requires: R-R6
Requires: R-checkmate
Requires: R-matrixStats
Requires: R-posterior
Requires: R-callr
Requires: R-processx
Requires: R-Rdpack
Requires: R-farver
Requires: R-labeling
Requires: R-RColorBrewer
Requires: R-viridisLite
Requires: R-backports
Requires: R-abind
Requires: R-tibble
Requires: R-tensorA
Requires: R-pillar
Requires: R-distributional
Requires: R-ps
Requires: R-rbibutils
Requires: R-generics
Requires: R-numDeriv
Requires: R-utf8
Requires: R-pkgconfig
# %%if 0%%{?sle_version} > 120400 || 0%%{?is_opensuse}
# # Three others commonly needed
# BuildRequires: tex(ae.sty)
# BuildRequires: tex(fancyvrb.sty)
# BuildRequires: tex(inconsolata.sty)
# BuildRequires: tex(natbib.sty)
# %else
# BuildRequires: texlive
# %endif
# BuildRequires: texinfo
BuildRequires: fdupes
BuildRequires: R-base
BuildRequires: R-lme4
BuildRequires: R-bigmemory
BuildRequires: R-Rcpp-devel
BuildRequires: R-ggplot2
BuildRequires: R-ncvreg
BuildRequires: R-reshape2
BuildRequires: R-rstan-devel
BuildRequires: R-stringr
BuildRequires: R-mvtnorm
BuildRequires: R-rstantools
BuildRequires: R-RcppParallel-devel
BuildRequires: R-BH-devel
BuildRequires: R-RcppArmadillo-devel
BuildRequires: R-RcppEigen-devel
BuildRequires: R-StanHeaders-devel
BuildRequires: R-bigmemory.sri
BuildRequires: R-uuid
BuildRequires: R-cli
BuildRequires: R-gtable
BuildRequires: R-isoband
BuildRequires: R-lifecycle
BuildRequires: R-rlang
BuildRequires: R-S7
BuildRequires: R-scales
BuildRequires: R-vctrs
BuildRequires: R-withr
BuildRequires: R-minqa
BuildRequires: R-nloptr
BuildRequires: R-reformulas
BuildRequires: R-plyr
BuildRequires: R-inline
BuildRequires: R-gridExtra
BuildRequires: R-loo
BuildRequires: R-pkgbuild
BuildRequires: R-QuickJSR-devel
BuildRequires: R-desc
BuildRequires: R-glue
BuildRequires: R-magrittr
BuildRequires: R-stringi
BuildRequires: R-R6
BuildRequires: R-checkmate
BuildRequires: R-matrixStats
BuildRequires: R-posterior
BuildRequires: R-callr
BuildRequires: R-processx
BuildRequires: R-Rdpack
BuildRequires: R-farver
BuildRequires: R-labeling
BuildRequires: R-RColorBrewer
BuildRequires: R-viridisLite
BuildRequires: R-backports
BuildRequires: R-abind
BuildRequires: R-tibble
BuildRequires: R-tensorA
BuildRequires: R-pillar
BuildRequires: R-distributional
BuildRequires: R-ps
BuildRequires: R-rbibutils
BuildRequires: R-generics
BuildRequires: R-numDeriv
BuildRequires: R-utf8
BuildRequires: R-pkgconfig
BuildRequires: gcc gcc-c++ gcc-fortran
Suggests: R-testthat
Suggests: R-knitr
Suggests: R-rmarkdown
%description
Fits high dimensional penalized generalized linear mixed models using
the Monte Carlo Expectation Conditional Minimization (MCECM) algorithm.
The purpose of the package is to perform variable selection on both the
fixed and random effects simultaneously for generalized linear mixed
models. The package supports fitting of Binomial, Gaussian, and Poisson
data with canonical links, and supports penalization using the MCP,
SCAD, or LASSO penalties. The MCECM algorithm is described in Rashid et
al. (2020) <doi:10.1080/01621459.2019.1671197>. The techniques used in
the minimization portion of the procedure (the M-step) are derived from
the procedures of the 'ncvreg' package (Breheny and Huang (2011)
<doi:10.1214/10-AOAS388>) and 'grpreg' package (Breheny and Huang
(2015) <doi:10.1007/s11222-013-9424-2>), with appropriate modifications
to account for the estimation and penalization of the random effects.
The 'ncvreg' and 'grpreg' packages also describe the MCP, SCAD, and
LASSO penalties.
%prep
%setup -q -c -n %{packname}
# the next line is needed, because we build without --clean in between two packages
rm -rf ~/.R
%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
%fdupes -s %{buildroot}%{rlibdir}
#%%check
#%%{_bindir}/R CMD check %%{packname}
%files
%dir %{rlibdir}/%{packname}
%doc %{rlibdir}/%{packname}/DESCRIPTION
%{rlibdir}/%{packname}/INDEX
%{rlibdir}/%{packname}/Meta
%{rlibdir}/%{packname}/NAMESPACE
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/data
%{rlibdir}/%{packname}/glmmPen_1.5.4.8.pdf
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%{rlibdir}/%{packname}/include
%{rlibdir}/%{packname}/libs
%{rlibdir}/%{packname}/stan
%{rlibdir}/%{packname}/update.R
%changelog
