File R-graphsim.spec of Package R-graphsim

# Automatically generated by CRAN2OBS
# 
# Spec file for package graphsim 
# 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) 2026 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  graphsim 
%global rlibdir   %{_libdir}/R/library 
 
Name:           R-%{packname} 
Version:        1.0.4 
Release:        0 
Summary:        Simulate Expression Data from 'igraph' Networks 
Group:          Development/Libraries/Other 
License:        GPL-3 
URL:            http://cran.r-project.org/web/packages/%{packname} 
Source:         graphsim_1.0.4.tar.gz 
Requires:       R-base 
Requires:	R-gplots
Requires:	R-igraph
Requires:	R-mvtnorm
Requires:	R-matrixcalc
Requires:	R-gtools
Requires:	R-caTools
Requires:	R-cli
Requires:	R-lifecycle
Requires:	R-magrittr
Requires:	R-pkgconfig
Requires:	R-rlang
Requires:	R-vctrs
Requires:	R-cpp11
Requires:	R-bitops
Requires:	R-glue
 
# %%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-gplots
BuildRequires: 	R-igraph
BuildRequires: 	R-mvtnorm
BuildRequires: 	R-matrixcalc
BuildRequires: 	R-gtools
BuildRequires: 	R-caTools
BuildRequires: 	R-cli
BuildRequires: 	R-lifecycle
BuildRequires: 	R-magrittr
BuildRequires: 	R-pkgconfig
BuildRequires: 	R-rlang
BuildRequires: 	R-vctrs
BuildRequires: 	R-cpp11-devel
BuildRequires: 	R-bitops
BuildRequires: 	R-glue
 
Suggests:	R-devtools
Suggests:	R-knitr
Suggests:	R-markdown
Suggests:	R-prettydoc
Suggests:	R-R.rsp
Suggests:	R-rmarkdown
Suggests:	R-testthat
Suggests:	R-scales
Suggests:	R-vdiffr
%description 
Functions to develop simulated continuous data (e.g., gene expression) 
from a sigma covariance matrix derived from a graph structure in 
'igraph' objects. Intended to extend 'mvtnorm' to take 'igraph' 
structures rather than sigma matrices as input. This allows the use of 
simulated data that correctly accounts for pathway relationships and 
correlations. This allows the use of simulated data that correctly 
accounts for pathway relationships and correlations. Here we present a 
versatile statistical framework to simulate correlated gene expression 
data from biological pathways, by sampling from a multivariate normal 
distribution derived from a graph structure. This package allows the 
simulation of biological pathways from a graph structure based on a 
statistical model of gene expression. For example methods to infer 
biological pathways and gene regulatory networks from gene expression 
data can be tested on simulated datasets using this framework. This 
also allows for pathway structures to be considered as a confounding 
variable when simulating gene expression data to test the performance 
of genomic analyses. 
 
%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} 
%{rlibdir}/%{packname}/CITATION
%doc %{rlibdir}/%{packname}/DESCRIPTION
%{rlibdir}/%{packname}/INDEX
%{rlibdir}/%{packname}/Meta
%{rlibdir}/%{packname}/NAMESPACE
%doc %{rlibdir}/%{packname}/NEWS.md
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/data
%doc %{rlibdir}/%{packname}/doc
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%{rlibdir}/%{packname}/resources
%doc %{rlibdir}/%{packname}/rmarkdown
 
%changelog