File R-SNPassoc.spec of Package R-SNPassoc

# Automatically generated by CRAN2OBS
# 
# Spec file for package SNPassoc 
# 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/ 
# 
 
%global packname  SNPassoc 
%global rlibdir   %{_libdir}/R/library 
 
Name:           R-%{packname} 
Version:        2.1.2 
Release:        0 
Summary:        SNPs-Based Whole Genome Association Studies 
Group:          Development/Libraries/Other 
License:        GPL (>= 2) 
URL:            http://cran.r-project.org/web/packages/%{packname} 
Source:         SNPassoc_2.1-2.tar.gz 
Requires:       R-base 
Requires:	R-haplo.stats
Requires:	R-mvtnorm
Requires:	R-tidyr
Requires:	R-plyr
Requires:	R-ggplot2
Requires:	R-poisbinom
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-arsenal
Requires:	R-rms
Requires:	R-Rcpp
Requires:	R-dplyr
Requires:	R-glue
Requires:	R-magrittr
Requires:	R-purrr
Requires:	R-stringr
Requires:	R-tibble
Requires:	R-tidyselect
Requires:	R-cpp11
Requires:	R-knitr
Requires:	R-generics
Requires:	R-pillar
Requires:	R-R6
Requires:	R-Hmisc
Requires:	R-quantreg
Requires:	R-SparseM
Requires:	R-polspline
Requires:	R-multcomp
Requires:	R-htmlTable
Requires:	R-htmltools
Requires:	R-digest
Requires:	R-colorspace
Requires:	R-farver
Requires:	R-labeling
Requires:	R-RColorBrewer
Requires:	R-viridisLite
Requires:	R-stringi
Requires:	R-pkgconfig
Requires:	R-gridExtra
Requires:	R-data.table
Requires:	R-viridis
Requires:	R-base64enc
Requires:	R-rmarkdown
Requires:	R-Formula
Requires:	R-checkmate
Requires:	R-htmlwidgets
Requires:	R-rstudioapi
Requires:	R-fastmap
Requires:	R-evaluate
Requires:	R-highr
Requires:	R-xfun
Requires:	R-yaml
Requires:	R-TH.data
Requires:	R-sandwich
Requires:	R-utf8
Requires:	R-MatrixModels
Requires:	R-backports
Requires:	R-jsonlite
Requires:	R-bslib
Requires:	R-fontawesome
Requires:	R-jquerylib
Requires:	R-tinytex
Requires:	R-zoo
Requires:	R-cachem
Requires:	R-memoise
Requires:	R-mime
Requires:	R-sass
Requires:	R-fs
Requires:	R-rappdirs
 
# %%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-haplo.stats
BuildRequires: 	R-mvtnorm
BuildRequires: 	R-tidyr
BuildRequires: 	R-plyr
BuildRequires: 	R-ggplot2
BuildRequires: 	R-poisbinom
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-arsenal
BuildRequires: 	R-rms
BuildRequires: 	R-Rcpp-devel
BuildRequires: 	R-dplyr
BuildRequires: 	R-glue
BuildRequires: 	R-magrittr
BuildRequires: 	R-purrr
BuildRequires: 	R-stringr
BuildRequires: 	R-tibble
BuildRequires: 	R-tidyselect
BuildRequires: 	R-cpp11-devel
BuildRequires: 	R-knitr
BuildRequires: 	R-generics
BuildRequires: 	R-pillar
BuildRequires: 	R-R6
BuildRequires: 	R-Hmisc
BuildRequires: 	R-quantreg
BuildRequires: 	R-SparseM
BuildRequires: 	R-polspline
BuildRequires: 	R-multcomp
BuildRequires: 	R-htmlTable
BuildRequires: 	R-htmltools
BuildRequires: 	R-digest
BuildRequires: 	R-colorspace
BuildRequires: 	R-farver
BuildRequires: 	R-labeling
BuildRequires: 	R-RColorBrewer
BuildRequires: 	R-viridisLite
BuildRequires: 	R-stringi
BuildRequires: 	R-pkgconfig
BuildRequires: 	R-gridExtra
BuildRequires: 	R-data.table
BuildRequires: 	R-viridis
BuildRequires: 	R-base64enc
BuildRequires: 	R-rmarkdown
BuildRequires: 	R-Formula
BuildRequires: 	R-checkmate
BuildRequires: 	R-htmlwidgets
BuildRequires: 	R-rstudioapi
BuildRequires: 	R-fastmap
BuildRequires: 	R-evaluate
BuildRequires: 	R-highr
BuildRequires: 	R-xfun
BuildRequires: 	R-yaml
BuildRequires: 	R-TH.data
BuildRequires: 	R-sandwich
BuildRequires: 	R-utf8
BuildRequires: 	R-MatrixModels
BuildRequires: 	R-backports
BuildRequires: 	R-jsonlite
BuildRequires: 	R-bslib
BuildRequires: 	R-fontawesome
BuildRequires: 	R-jquerylib
BuildRequires: 	R-tinytex
BuildRequires: 	R-zoo
BuildRequires: 	R-cachem
BuildRequires: 	R-memoise
BuildRequires: 	R-mime
BuildRequires: 	R-sass
BuildRequires: 	R-fs
BuildRequires: 	R-rappdirs
 
Suggests:	R-testthat
Suggests:	R-knitr
Suggests:	R-rmarkdown
Suggests:	R-biomaRt
Suggests:	R-VariantAnnotation
Suggests:	R-GenomicRanges
Suggests:	R-IRanges
Suggests:	R-S4Vectors
Suggests:	R-org.Hs.eg.db
Suggests:	R-TxDb.Hsapiens.UCSC.hg19.knownGene
%description 
Functions to perform most of the common analysis in genome association 
studies are implemented. These analyses include descriptive statistics 
and exploratory analysis of missing values, calculation of 
Hardy-Weinberg equilibrium, analysis of association based on 
generalized linear models (either for quantitative or binary traits), 
and analysis of multiple SNPs (haplotype and epistasis analysis). 
Permutation test and related tests (sum statistic and truncated 
product) are also implemented. Max-statistic and genetic risk-allele 
score exact distributions are also possible to be estimated. The 
methods are described in Gonzalez JR et al., 2007 <doi: 
10.1093/bioinformatics/btm025>. 
 
%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
%{rlibdir}/%{packname}/docs
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
 
%changelog