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File R-aSPU.spec of Package R-aSPU (Revision 8a93bf41339b5b8f8ad41d8ab7407975)

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# Automatically generated by CRAN2OBS
# 
# Spec file for package aSPU 
# 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) 2022 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/ 
# 
 
%global packname  aSPU 
%global rlibdir   %{_libdir}/R/library 
 
Name:           R-%{packname} 
Version:        1.50 
Release:        0 
Summary:        Adaptive Sum of Powered Score Test 
Group:          Development/Libraries/Other 
License:        GPL-3 
URL:            http://cran.r-project.org/web/packages/%{packname} 
Source:         aSPU_1.50.tar.gz 
Requires:       R-base 
Requires:	R-gee
Requires:	R-mvtnorm
Requires:	R-fields
Requires:	R-matrixStats
Requires:	R-spam
Requires:	R-viridis
Requires:	R-maps
Requires:	R-dotCall64
Requires:	R-viridisLite
Requires:	R-ggplot2
Requires:	R-gridExtra
Requires:	R-digest
Requires:	R-glue
Requires:	R-gtable
Requires:	R-isoband
Requires:	R-rlang
Requires:	R-scales
Requires:	R-tibble
Requires:	R-withr
Requires:	R-farver
Requires:	R-labeling
Requires:	R-lifecycle
Requires:	R-munsell
Requires:	R-R6
Requires:	R-RColorBrewer
Requires:	R-fansi
Requires:	R-magrittr
Requires:	R-pillar
Requires:	R-pkgconfig
Requires:	R-vctrs
Requires:	R-cli
Requires:	R-colorspace
Requires:	R-utf8
 
# %%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-gee
BuildRequires: 	R-mvtnorm
BuildRequires: 	R-fields
BuildRequires: 	R-matrixStats
BuildRequires: 	R-spam
BuildRequires: 	R-viridis
BuildRequires: 	R-maps
BuildRequires: 	R-dotCall64
BuildRequires: 	R-viridisLite
BuildRequires: 	R-ggplot2
BuildRequires: 	R-gridExtra
BuildRequires: 	R-digest
BuildRequires: 	R-glue
BuildRequires: 	R-gtable
BuildRequires: 	R-isoband
BuildRequires: 	R-rlang
BuildRequires: 	R-scales
BuildRequires: 	R-tibble
BuildRequires: 	R-withr
BuildRequires: 	R-farver
BuildRequires: 	R-labeling
BuildRequires: 	R-lifecycle
BuildRequires: 	R-munsell
BuildRequires: 	R-R6
BuildRequires: 	R-RColorBrewer
BuildRequires: 	R-fansi
BuildRequires: 	R-magrittr
BuildRequires: 	R-pillar
BuildRequires: 	R-pkgconfig
BuildRequires: 	R-vctrs
BuildRequires: 	R-cli
BuildRequires: 	R-colorspace
BuildRequires: 	R-utf8
 
Suggests:	R-rmarkdown
Suggests:	R-markdown
Suggests:	R-knitr
%description 
R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') 
tests, inverse variance weighted Sum of Powered score ('SPUw' and 
'aSPUw') tests and gene-based and some pathway based association tests 
(Pathway based Sum of Powered Score tests ('SPUpath'), adaptive 
'SPUpath' ('aSPUpath') test, 'GEEaSPU' test for multiple traits - 
single 'SNP' (single nucleotide polymorphism) association in 
generalized estimation equations, 'MTaSPUs' test for multiple traits - 
single 'SNP' association with Genome Wide Association Studies ('GWAS') 
summary statistics, Gene-based Association Test that uses an extended 
'Simes' procedure ('GATES'), Hybrid Set-based Test ('HYST') and 
extended version of 'GATES' test for pathway-based association testing 
('GATES-Simes'). ). The tests can be used with genetic and other data 
sets with covariates. The response variable is binary or quantitative. 
Summary; (1) Single trait-'SNP' set association with individual-level 
data ('aSPU', 'aSPUw', 'aSPUr'), (2) Single trait-'SNP' set association 
with summary statistics ('aSPUs'), (3) Single trait-pathway association 
with individual-level data ('aSPUpath'), (4) Single trait-pathway 
association with summary statistics ('aSPUsPath'), (5) Multiple 
traits-single 'SNP' association with individual-level data ('GEEaSPU'), 
(6) Multiple traits- single 'SNP' association with summary statistics 
('MTaSPUs'), (7) Multiple traits-'SNP' set association with summary 
statistics('MTaSPUsSet'), (8) Multiple traits-pathway association with 
summary statistics('MTaSPUsSetPath'). 
 
%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}/doc
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
 
%changelog

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File R-aSPU.spec of Package R-aSPU (Revision 8a93bf41339b5b8f8ad41d8ab7407975)

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