File R-ActivePathways.spec of Package R-ActivePathways

# Automatically generated by CRAN2OBS
# 
# Spec file for package ActivePathways 
# 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. 
# 
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# 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. 
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# Please submit bugfixes or comments via http://bugs.opensuse.org/ 
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%global packname  ActivePathways 
%global rlibdir   %{_libdir}/R/library 
 
Name:           R-%{packname} 
Version:        2.0.6 
Release:        0 
Summary:        Integrative Pathway Enrichment Analysis of Multivariate Omics Data 
Group:          Development/Libraries/Other 
License:        GPL-3 
URL:            http://cran.r-project.org/web/packages/%{packname} 
Source:         ActivePathways_2.0.6.tar.gz 
Requires:       R-base 
Requires:	R-data.table
Requires:	R-ggplot2
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-glue
Requires:	R-cpp11
Requires:	R-farver
Requires:	R-labeling
Requires:	R-R6
Requires:	R-RColorBrewer
Requires:	R-viridisLite
 
# %%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-ggplot2
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-glue
BuildRequires: 	R-cpp11-devel
BuildRequires: 	R-farver
BuildRequires: 	R-labeling
BuildRequires: 	R-R6
BuildRequires: 	R-RColorBrewer
BuildRequires: 	R-viridisLite
 
Suggests:	R-testthat
Suggests:	R-knitr
Suggests:	R-rmarkdown
Suggests:	R-RColorBrewer
%description 
Framework for analysing multiple omics datasets in the context of 
molecular pathways, biological processes and other types of gene sets. 
The package uses p-value merging to combine gene- or protein-level 
signals, followed by ranked hypergeometric tests to determine enriched 
pathways and processes. Genes can be integrated using directional 
constraints that reflect how the input datasets are expected interact 
with one another. This approach allows researchers to interpret a 
series of omics datasets in the context of known biology and gene 
function, and discover associations that are only apparent when several 
datasets are combined. The recent version of the package is part of the 
following publication: Directional integration and pathway enrichment 
analysis for multi-omics data. Slobodyanyuk M^, Bahcheli AT^, Klein ZP, 
Bayati M, Strug LJ, Reimand J. Nature Communications (2024) 
<doi:10.1038/s41467-024-49986-4>. 
 
%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
%doc %{rlibdir}/%{packname}/NEWS.md
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/doc
%{rlibdir}/%{packname}/extdata
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
 
%changelog