Overview

File R-SlideCNA.spec of Package R-SlideCNA

# Automatically generated by CRAN2OBS
# 
# Spec file for package SlideCNA 
# 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  SlideCNA 
%global rlibdir   %{_libdir}/R/library 
 
Name:           R-%{packname} 
Version:        0.1.0 
Release:        0 
Summary:        Calls Copy Number Alterations from Slide-Seq Data 
Group:          Development/Libraries/Other 
License:        GPL (>= 3) 
URL:            http://cran.r-project.org/web/packages/%{packname} 
Source:         SlideCNA_0.1.0.tar.gz 
Requires:       R-base 
Requires:	R-data.table
Requires:	R-reshape2
Requires:	R-dplyr
Requires:	R-ggplot2
Requires:	R-scales
Requires:	R-pheatmap
Requires:	R-factoextra
Requires:	R-dendextend
Requires:	R-Seurat
Requires:	R-tidyselect
Requires:	R-stringr
Requires:	R-magrittr
Requires:	R-tibble
Requires:	R-futile.logger
Requires:	R-mltools
Requires:	R-viridis
Requires:	R-cli
Requires:	R-generics
Requires:	R-glue
Requires:	R-lifecycle
Requires:	R-pillar
Requires:	R-R6
Requires:	R-rlang
Requires:	R-vctrs
Requires:	R-abind
Requires:	R-FactoMineR
Requires:	R-ggpubr
Requires:	R-ggrepel
Requires:	R-tidyr
Requires:	R-lambda.r
Requires:	R-futile.options
Requires:	R-gtable
Requires:	R-isoband
Requires:	R-withr
Requires:	R-RColorBrewer
Requires:	R-plyr
Requires:	R-Rcpp
Requires:	R-farver
Requires:	R-labeling
Requires:	R-viridisLite
Requires:	R-SeuratObject
Requires:	R-cowplot
Requires:	R-fastDummies
Requires:	R-fitdistrplus
Requires:	R-future
Requires:	R-future.apply
Requires:	R-ggridges
Requires:	R-httr
Requires:	R-ica
Requires:	R-igraph
Requires:	R-irlba
Requires:	R-jsonlite
Requires:	R-leidenbase
Requires:	R-lmtest
Requires:	R-matrixStats
Requires:	R-miniUI
Requires:	R-patchwork
Requires:	R-pbapply
Requires:	R-plotly
Requires:	R-png
Requires:	R-progressr
Requires:	R-RANN
Requires:	R-RcppAnnoy
Requires:	R-RcppHNSW
Requires:	R-reticulate
Requires:	R-ROCR
Requires:	R-RSpectra
Requires:	R-Rtsne
Requires:	R-scattermore
Requires:	R-sctransform
Requires:	R-shiny
Requires:	R-spatstat.explore
Requires:	R-spatstat.geom
Requires:	R-uwot
Requires:	R-RcppEigen
Requires:	R-RcppProgress
Requires:	R-stringi
Requires:	R-pkgconfig
Requires:	R-car
Requires:	R-DT
Requires:	R-ellipse
Requires:	R-emmeans
Requires:	R-flashClust
Requires:	R-leaps
Requires:	R-multcompView
Requires:	R-scatterplot3d
Requires:	R-digest
Requires:	R-globals
Requires:	R-listenv
Requires:	R-parallelly
Requires:	R-ggsci
Requires:	R-purrr
Requires:	R-ggsignif
Requires:	R-gridExtra
Requires:	R-polynom
Requires:	R-rstatix
Requires:	R-curl
Requires:	R-mime
Requires:	R-openssl
Requires:	R-cpp11
Requires:	R-formatR
Requires:	R-zoo
Requires:	R-htmltools
Requires:	R-utf8
Requires:	R-base64enc
Requires:	R-htmlwidgets
Requires:	R-lazyeval
Requires:	R-crosstalk
Requires:	R-promises
Requires:	R-RcppTOML
Requires:	R-here
Requires:	R-rappdirs
Requires:	R-gplots
Requires:	R-RcppArmadillo
Requires:	R-sp
Requires:	R-spam
Requires:	R-httpuv
Requires:	R-xtable
Requires:	R-fontawesome
Requires:	R-sourcetools
Requires:	R-later
Requires:	R-crayon
Requires:	R-fastmap
Requires:	R-commonmark
Requires:	R-bslib
Requires:	R-cachem
Requires:	R-spatstat.data
Requires:	R-spatstat.univar
Requires:	R-spatstat.random
Requires:	R-spatstat.utils
Requires:	R-spatstat.sparse
Requires:	R-goftest
Requires:	R-deldir
Requires:	R-polyclip
Requires:	R-FNN
Requires:	R-dqrng
Requires:	R-jquerylib
Requires:	R-memoise
Requires:	R-sass
Requires:	R-carData
Requires:	R-Formula
Requires:	R-pbkrtest
Requires:	R-quantreg
Requires:	R-lme4
Requires:	R-BH
Requires:	R-sitmo
Requires:	R-estimability
Requires:	R-mvtnorm
Requires:	R-numDeriv
Requires:	R-gtools
Requires:	R-caTools
Requires:	R-rprojroot
Requires:	R-knitr
Requires:	R-rmarkdown
Requires:	R-yaml
Requires:	R-askpass
Requires:	R-broom
Requires:	R-corrplot
Requires:	R-dotCall64
Requires:	R-tensor
Requires:	R-sys
Requires:	R-backports
Requires:	R-bitops
Requires:	R-evaluate
Requires:	R-highr
Requires:	R-xfun
Requires:	R-minqa
Requires:	R-nloptr
Requires:	R-reformulas
Requires:	R-doBy
Requires:	R-SparseM
Requires:	R-MatrixModels
Requires:	R-tinytex
Requires:	R-fs
Requires:	R-Deriv
Requires:	R-modelr
Requires:	R-microbenchmark
Requires:	R-Rdpack
Requires:	R-rbibutils
 
# %%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-reshape2
BuildRequires: 	R-dplyr
BuildRequires: 	R-ggplot2
BuildRequires: 	R-scales
BuildRequires: 	R-pheatmap
BuildRequires: 	R-factoextra
BuildRequires: 	R-dendextend
BuildRequires: 	R-Seurat
BuildRequires: 	R-tidyselect
BuildRequires: 	R-stringr
BuildRequires: 	R-magrittr
BuildRequires: 	R-tibble
BuildRequires: 	R-futile.logger
BuildRequires: 	R-mltools
BuildRequires: 	R-viridis
BuildRequires: 	R-cli
BuildRequires: 	R-generics
BuildRequires: 	R-glue
BuildRequires: 	R-lifecycle
BuildRequires: 	R-pillar
BuildRequires: 	R-R6
BuildRequires: 	R-rlang
BuildRequires: 	R-vctrs
BuildRequires: 	R-abind
BuildRequires: 	R-FactoMineR
BuildRequires: 	R-ggpubr
BuildRequires: 	R-ggrepel
BuildRequires: 	R-tidyr
BuildRequires: 	R-lambda.r
BuildRequires: 	R-futile.options
BuildRequires: 	R-gtable
BuildRequires: 	R-isoband
BuildRequires: 	R-withr
BuildRequires: 	R-RColorBrewer
BuildRequires: 	R-plyr
BuildRequires: 	R-Rcpp-devel
BuildRequires: 	R-farver
BuildRequires: 	R-labeling
BuildRequires: 	R-viridisLite
BuildRequires: 	R-SeuratObject
BuildRequires: 	R-cowplot
BuildRequires: 	R-fastDummies
BuildRequires: 	R-fitdistrplus
BuildRequires: 	R-future
BuildRequires: 	R-future.apply
BuildRequires: 	R-ggridges
BuildRequires: 	R-httr
BuildRequires: 	R-ica
BuildRequires: 	R-igraph
BuildRequires: 	R-irlba
BuildRequires: 	R-jsonlite
BuildRequires: 	R-leidenbase
BuildRequires: 	R-lmtest
BuildRequires: 	R-matrixStats
BuildRequires: 	R-miniUI
BuildRequires: 	R-patchwork
BuildRequires: 	R-pbapply
BuildRequires: 	R-plotly
BuildRequires: 	R-png
BuildRequires: 	R-progressr
BuildRequires: 	R-RANN
BuildRequires: 	R-RcppAnnoy
BuildRequires: 	R-RcppHNSW
BuildRequires: 	R-reticulate
BuildRequires: 	R-ROCR
BuildRequires: 	R-RSpectra-devel
BuildRequires: 	R-Rtsne
BuildRequires: 	R-scattermore
BuildRequires: 	R-sctransform
BuildRequires: 	R-shiny
BuildRequires: 	R-spatstat.explore
BuildRequires: 	R-spatstat.geom
BuildRequires: 	R-uwot-devel
BuildRequires: 	R-RcppEigen-devel
BuildRequires: 	R-RcppProgress
BuildRequires: 	R-stringi
BuildRequires: 	R-pkgconfig
BuildRequires: 	R-car
BuildRequires: 	R-DT
BuildRequires: 	R-ellipse
BuildRequires: 	R-emmeans
BuildRequires: 	R-flashClust
BuildRequires: 	R-leaps
BuildRequires: 	R-multcompView
BuildRequires: 	R-scatterplot3d
BuildRequires: 	R-digest
BuildRequires: 	R-globals
BuildRequires: 	R-listenv
BuildRequires: 	R-parallelly
BuildRequires: 	R-ggsci
BuildRequires: 	R-purrr
BuildRequires: 	R-ggsignif
BuildRequires: 	R-gridExtra
BuildRequires: 	R-polynom
BuildRequires: 	R-rstatix
BuildRequires: 	R-curl
BuildRequires: 	R-mime
BuildRequires: 	R-openssl
BuildRequires: 	R-cpp11-devel
BuildRequires: 	R-formatR
BuildRequires: 	R-zoo
BuildRequires: 	R-htmltools
BuildRequires: 	R-utf8
BuildRequires: 	R-base64enc
BuildRequires: 	R-htmlwidgets
BuildRequires: 	R-lazyeval
BuildRequires: 	R-crosstalk
BuildRequires: 	R-promises
BuildRequires: 	R-RcppTOML-devel
BuildRequires: 	R-here
BuildRequires: 	R-rappdirs
BuildRequires: 	R-gplots
BuildRequires: 	R-RcppArmadillo-devel
BuildRequires: 	R-sp
BuildRequires: 	R-spam
BuildRequires: 	R-httpuv
BuildRequires: 	R-xtable
BuildRequires: 	R-fontawesome
BuildRequires: 	R-sourcetools-devel
BuildRequires: 	R-later
BuildRequires: 	R-crayon
BuildRequires: 	R-fastmap
BuildRequires: 	R-commonmark
BuildRequires: 	R-bslib
BuildRequires: 	R-cachem
BuildRequires: 	R-spatstat.data
BuildRequires: 	R-spatstat.univar
BuildRequires: 	R-spatstat.random
BuildRequires: 	R-spatstat.utils
BuildRequires: 	R-spatstat.sparse
BuildRequires: 	R-goftest
BuildRequires: 	R-deldir
BuildRequires: 	R-polyclip
BuildRequires: 	R-FNN
BuildRequires: 	R-dqrng
BuildRequires: 	R-jquerylib
BuildRequires: 	R-memoise
BuildRequires: 	R-sass
BuildRequires: 	R-carData
BuildRequires: 	R-Formula
BuildRequires: 	R-pbkrtest
BuildRequires: 	R-quantreg
BuildRequires: 	R-lme4
BuildRequires: 	R-BH-devel
BuildRequires: 	R-sitmo
BuildRequires: 	R-estimability
BuildRequires: 	R-mvtnorm
BuildRequires: 	R-numDeriv
BuildRequires: 	R-gtools
BuildRequires: 	R-caTools
BuildRequires: 	R-rprojroot
BuildRequires: 	R-knitr
BuildRequires: 	R-rmarkdown
BuildRequires: 	R-yaml
BuildRequires: 	R-askpass
BuildRequires: 	R-broom
BuildRequires: 	R-corrplot
BuildRequires: 	R-dotCall64
BuildRequires: 	R-tensor
BuildRequires: 	R-sys
BuildRequires: 	R-backports
BuildRequires: 	R-bitops
BuildRequires: 	R-evaluate
BuildRequires: 	R-highr
BuildRequires: 	R-xfun
BuildRequires: 	R-minqa
BuildRequires: 	R-nloptr
BuildRequires: 	R-reformulas
BuildRequires: 	R-doBy
BuildRequires: 	R-SparseM
BuildRequires: 	R-MatrixModels
BuildRequires: 	R-tinytex
BuildRequires: 	R-fs
BuildRequires: 	R-Deriv
BuildRequires: 	R-modelr
BuildRequires: 	R-microbenchmark
BuildRequires: 	R-Rdpack
BuildRequires: 	R-rbibutils
 
Suggests:	R-testthat
Suggests:	R-enrichR
%description 
This takes spatial single-cell-type RNA-seq data (specifically designed 
for Slide-seq v2) that calls copy number alterations (CNAs) using 
pseudo-spatial binning, clusters cellular units (e.g. beads) based on 
CNA profile, and visualizes spatial CNA patterns. Documentation about 
'SlideCNA' is included in the the pre-print by Zhang et al. (2022, 
<doi:10.1101/2022.11.25.517982>). The package 'enrichR' (>= 3.0), 
conditionally used to annotate SlideCNA-determined clusters with gene 
ontology terms, can be installed at 
<https://github.com/wjawaid/enrichR> or with 
install_github("wjawaid/enrichR"). 
 
%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}/SlideCNA_env.yml
%{rlibdir}/%{packname}/bead_split_env.yml
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
 
%changelog
openSUSE Build Service is sponsored by
Places