File R-kdps.spec of Package R-kdps

# Automatically generated by CRAN2OBS
# 
# Spec file for package kdps 
# This file is auto-generated using information in the package source, 
# esp. Description and Summary. Improvements in that area should be 
# discussed with upstream. 
# 
# Copyright (c) 2025 SUSE LINUX GmbH, Nuernberg, Germany. 
# 
# All modifications and additions to the file contributed by third parties 
# remain the property of their copyright owners, unless otherwise agreed 
# upon. The license for this file, and modifications and additions to the 
# file, is the same license as for the pristine package itself (unless the 
# license for the pristine package is not an Open Source License, in which 
# case the license is the MIT License). An "Open Source License" is a 
# license that conforms to the Open Source Definition (Version 1.9) 
# published by the Open Source Initiative. 
#  
# Please submit bugfixes or comments via http://bugs.opensuse.org/ 
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%global packname  kdps 
%global rlibdir   %{_libdir}/R/library 
 
Name:           R-%{packname} 
Version:        1.0.0 
Release:        0 
Summary:        Kinship Decouple and Phenotype Selection (KDPS) 
Group:          Development/Libraries/Other 
License:        MIT + file LICENSE 
URL:            http://cran.r-project.org/web/packages/%{packname} 
Source:         kdps_1.0.0.tar.gz 
Requires:       R-base 
Requires:	R-data.table
Requires:	R-dplyr
Requires:	R-progress
Requires:	R-tibble
Requires:	R-cli
Requires:	R-generics
Requires:	R-glue
Requires:	R-lifecycle
Requires:	R-magrittr
Requires:	R-pillar
Requires:	R-R6
Requires:	R-rlang
Requires:	R-tidyselect
Requires:	R-vctrs
Requires:	R-crayon
Requires:	R-hms
Requires:	R-prettyunits
Requires:	R-pkgconfig
Requires:	R-utf8
Requires:	R-withr
 
# %%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-data.table
BuildRequires: 	R-dplyr
BuildRequires: 	R-progress
BuildRequires: 	R-tibble
BuildRequires: 	R-cli
BuildRequires: 	R-generics
BuildRequires: 	R-glue
BuildRequires: 	R-lifecycle
BuildRequires: 	R-magrittr
BuildRequires: 	R-pillar
BuildRequires: 	R-R6
BuildRequires: 	R-rlang
BuildRequires: 	R-tidyselect
BuildRequires: 	R-vctrs
BuildRequires: 	R-crayon
BuildRequires: 	R-hms
BuildRequires: 	R-prettyunits
BuildRequires: 	R-pkgconfig
BuildRequires: 	R-utf8
BuildRequires: 	R-withr
 
Suggests:	R-devtools
Suggests:	R-knitr
Suggests:	R-rmarkdown
%description 
A phenotype-aware algorithm for resolving cryptic relatedness in 
genetic studies. It removes related individuals based on kinship or 
identity-by-descent (IBD) scores while prioritizing subjects with 
phenotypes of interest. This approach helps maximize the retention of 
informative subjects, particularly for rare or valuable traits, and 
improves statistical power in genetic and epidemiological studies. KDPS 
supports both categorical and quantitative phenotypes, composite 
scoring, and customizable pruning strategies using a fuzziness 
parameter. Benchmark results show improved phenotype retention and high 
computational efficiency on large-scale datasets like the UK Biobank. 
Methods used include Manichaikul et al. (2010) 
<doi:10.1093/bioinformatics/btq559> for kinship estimation, Purcell et 
al. (2007) <doi:10.1086/519795> for IBD estimation, and Bycroft et al. 
(2018) <doi:10.1038/s41586-018-0579-z> for UK Biobank data reference. 
 
%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
%license %{rlibdir}/%{packname}/LICENSE
%{rlibdir}/%{packname}/Meta
%{rlibdir}/%{packname}/NAMESPACE
%{rlibdir}/%{packname}/R
%doc %{rlibdir}/%{packname}/doc
%{rlibdir}/%{packname}/extdata
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
 
%changelog