File R-CLONETv2.spec of Package R-CLONETv2

# Automatically generated by CRAN2OBS
# 
# Spec file for package CLONETv2 
# 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  CLONETv2 
%global rlibdir   %{_libdir}/R/library 
 
Name:           R-%{packname} 
Version:        2.2.1 
Release:        0 
Summary:        Clonality Estimates in Tumor 
Group:          Development/Libraries/Other 
License:        MIT + file LICENSE 
URL:            http://cran.r-project.org/web/packages/%{packname} 
Source:         CLONETv2_2.2.1.tar.gz 
Requires:       R-base 
Requires:	R-sets
Requires:	R-ggplot2
Requires:	R-ggrepel
Requires:	R-arules
Requires:	R-dbscan
Requires:	R-generics
Requires:	R-Rcpp
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-sets
BuildRequires: 	R-ggplot2
BuildRequires: 	R-ggrepel
BuildRequires: 	R-arules
BuildRequires: 	R-dbscan
BuildRequires: 	R-generics
BuildRequires: 	R-Rcpp-devel
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
 
%description 
Analyze data from next-generation sequencing experiments on genomic 
samples. 'CLONETv2' offers a set of functions to compute allele 
specific copy number and clonality from segmented data and SNPs 
position pileup. The package has also calculated the clonality of 
single nucleotide variants given read counts at mutated positions. The 
package has been developed at the laboratory of Computational and 
Functional Oncology, Department of CIBIO, University of Trento (Italy), 
under the supervision of prof Francesca Demichelis. References: Prandi 
et al. (2014) <doi:10.1186/s13059-014-0439-6>; Carreira et al. (2014) 
<doi:10.1126/scitranslmed.3009448>; Romanel et al. (2015) 
<doi:10.1126/scitranslmed.aac9511>. 
 
%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
%doc %{rlibdir}/%{packname}/NEWS.md
%{rlibdir}/%{packname}/R
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%{rlibdir}/%{packname}/sample.seg
%{rlibdir}/%{packname}/sample1.seg
%{rlibdir}/%{packname}/sample1_normal_pileup.tsv.gz
%{rlibdir}/%{packname}/sample1_snv_read_count.tsv
%{rlibdir}/%{packname}/sample1_tumor_pileup.tsv.gz
%{rlibdir}/%{packname}/sample2.seg
%{rlibdir}/%{packname}/sample2_normal_pileup.tsv.gz
%{rlibdir}/%{packname}/sample2_snv_read_count.tsv
%{rlibdir}/%{packname}/sample2_tumor_pileup.tsv.gz
%{rlibdir}/%{packname}/sample3.seg
%{rlibdir}/%{packname}/sample3_normal_pileup.tsv.gz
%{rlibdir}/%{packname}/sample3_snv_read_count.tsv
%{rlibdir}/%{packname}/sample3_tumor_pileup.tsv.gz
%{rlibdir}/%{packname}/sample4.seg
%{rlibdir}/%{packname}/sample4_normal_pileup.tsv.gz
%{rlibdir}/%{packname}/sample4_snv_read_count.tsv
%{rlibdir}/%{packname}/sample4_tumor_pileup.tsv.gz
%{rlibdir}/%{packname}/sample5.seg
%{rlibdir}/%{packname}/sample5_normal_pileup.tsv.gz
%{rlibdir}/%{packname}/sample5_snv_read_count.tsv
%{rlibdir}/%{packname}/sample5_tumor_pileup.tsv.gz
%{rlibdir}/%{packname}/sample_normal_pileup.tsv
%{rlibdir}/%{packname}/sample_snv_read_count.tsv
%{rlibdir}/%{packname}/sample_tumor_pileup.tsv
 
%changelog