openSUSE Build Service

Overview Repositories Revisions Requests Users Attributes Meta

File R-BED.spec of Package R-BED

# Automatically generated by CRAN2OBS
# 
# Spec file for package BED 
# 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) 2024 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  BED 
%global rlibdir   %{_libdir}/R/library 
 
Name:           R-%{packname} 
Version:        1.5.2 
Release:        0 
Summary:        Biological Entity Dictionary (BED) 
Group:          Development/Libraries/Other 
License:        GPL-3 
URL:            http://cran.r-project.org/web/packages/%{packname} 
Source:         BED_1.5.2.tar.gz 
Requires:       R-base 
Requires:	R-neo2R
Requires:	R-visNetwork
Requires:	R-dplyr
Requires:	R-readr
Requires:	R-stringr
Requires:	R-shiny
Requires:	R-DT
Requires:	R-miniUI
Requires:	R-rstudioapi
Requires:	R-cli
Requires:	R-generics
Requires:	R-glue
Requires:	R-lifecycle
Requires:	R-magrittr
Requires:	R-pillar
Requires:	R-R6
Requires:	R-rlang
Requires:	R-tibble
Requires:	R-tidyselect
Requires:	R-vctrs
Requires:	R-htmltools
Requires:	R-htmlwidgets
Requires:	R-httpuv
Requires:	R-jsonlite
Requires:	R-crosstalk
Requires:	R-jquerylib
Requires:	R-promises
Requires:	R-base64enc
Requires:	R-httr
Requires:	R-clipr
Requires:	R-crayon
Requires:	R-hms
Requires:	R-vroom
Requires:	R-cpp11
Requires:	R-tzdb
Requires:	R-mime
Requires:	R-xtable
Requires:	R-fontawesome
Requires:	R-sourcetools
Requires:	R-later
Requires:	R-fastmap
Requires:	R-withr
Requires:	R-commonmark
Requires:	R-bslib
Requires:	R-cachem
Requires:	R-stringi
Requires:	R-memoise
Requires:	R-sass
Requires:	R-lazyeval
Requires:	R-pkgconfig
Requires:	R-digest
Requires:	R-knitr
Requires:	R-rmarkdown
Requires:	R-yaml
Requires:	R-Rcpp
Requires:	R-curl
Requires:	R-openssl
Requires:	R-fansi
Requires:	R-utf8
Requires:	R-bit64
Requires:	R-progress
Requires:	R-bit
Requires:	R-evaluate
Requires:	R-highr
Requires:	R-xfun
Requires:	R-askpass
Requires:	R-prettyunits
Requires:	R-tinytex
Requires:	R-fs
Requires:	R-rappdirs
Requires:	R-sys
 
# %%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-neo2R
BuildRequires: 	R-visNetwork
BuildRequires: 	R-dplyr
BuildRequires: 	R-readr
BuildRequires: 	R-stringr
BuildRequires: 	R-shiny
BuildRequires: 	R-DT
BuildRequires: 	R-miniUI
BuildRequires: 	R-rstudioapi
BuildRequires: 	R-cli
BuildRequires: 	R-generics
BuildRequires: 	R-glue
BuildRequires: 	R-lifecycle
BuildRequires: 	R-magrittr
BuildRequires: 	R-pillar
BuildRequires: 	R-R6
BuildRequires: 	R-rlang
BuildRequires: 	R-tibble
BuildRequires: 	R-tidyselect
BuildRequires: 	R-vctrs
BuildRequires: 	R-htmltools
BuildRequires: 	R-htmlwidgets
BuildRequires: 	R-httpuv
BuildRequires: 	R-jsonlite
BuildRequires: 	R-crosstalk
BuildRequires: 	R-jquerylib
BuildRequires: 	R-promises
BuildRequires: 	R-base64enc
BuildRequires: 	R-httr
BuildRequires: 	R-clipr
BuildRequires: 	R-crayon
BuildRequires: 	R-hms
BuildRequires: 	R-vroom
BuildRequires: 	R-cpp11-devel
BuildRequires: 	R-tzdb
BuildRequires: 	R-mime
BuildRequires: 	R-xtable
BuildRequires: 	R-fontawesome
BuildRequires: 	R-sourcetools-devel
BuildRequires: 	R-later
BuildRequires: 	R-fastmap
BuildRequires: 	R-withr
BuildRequires: 	R-commonmark
BuildRequires: 	R-bslib
BuildRequires: 	R-cachem
BuildRequires: 	R-stringi
BuildRequires: 	R-memoise
BuildRequires: 	R-sass
BuildRequires: 	R-lazyeval
BuildRequires: 	R-pkgconfig
BuildRequires: 	R-digest
BuildRequires: 	R-knitr
BuildRequires: 	R-rmarkdown
BuildRequires: 	R-yaml
BuildRequires: 	R-Rcpp-devel
BuildRequires: 	R-curl
BuildRequires: 	R-openssl
BuildRequires: 	R-fansi
BuildRequires: 	R-utf8
BuildRequires: 	R-bit64
BuildRequires: 	R-progress
BuildRequires: 	R-bit
BuildRequires: 	R-evaluate
BuildRequires: 	R-highr
BuildRequires: 	R-xfun
BuildRequires: 	R-askpass
BuildRequires: 	R-prettyunits
BuildRequires: 	R-tinytex
BuildRequires: 	R-fs
BuildRequires: 	R-rappdirs
BuildRequires: 	R-sys
 
Suggests:	R-knitr
Suggests:	R-rmarkdown
Suggests:	R-biomaRt
Suggests:	R-GEOquery
Suggests:	R-base64enc
Suggests:	R-htmltools
Suggests:	R-webshot2
Suggests:	R-RCurl
%description 
An interface for the 'Neo4j' database providing mapping between 
different identifiers of biological entities. This Biological Entity 
Dictionary (BED) has been developed to address three main challenges. 
The first one is related to the completeness of identifier mappings. 
Indeed, direct mapping information provided by the different systems 
are not always complete and can be enriched by mappings provided by 
other resources. More interestingly, direct mappings not identified by 
any of these resources can be indirectly inferred by using mappings to 
a third reference. For example, many human Ensembl gene ID are not 
directly mapped to any Entrez gene ID but such mappings can be inferred 
using respective mappings to HGNC ID. The second challenge is related 
to the mapping of deprecated identifiers. Indeed, entity identifiers 
can change from one resource release to another. The identifier history 
is provided by some resources, such as Ensembl or the NCBI, but it is 
generally not used by mapping tools. The third challenge is related to 
the automation of the mapping process according to the relationships 
between the biological entities of interest. Indeed, mapping between 
gene and protein ID scopes should not be done the same way than between 
two scopes regarding gene ID. Also, converting identifiers from 
different organisms should be possible using gene orthologs 
information. The method has been published by Godard and van Eyll 
(2018) <doi:10.12688/f1000research.13925.3>. 
 
%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}/Documentation
%{rlibdir}/%{packname}/INDEX
%{rlibdir}/%{packname}/Meta
%{rlibdir}/%{packname}/NAMESPACE
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/doc
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%{rlibdir}/%{packname}/pkgdown.yml
%{rlibdir}/%{packname}/rstudio
%{rlibdir}/%{packname}/
 
%changelog

Places

File R-BED.spec of Package R-BED

Places