File R-TreeSearch.spec of Package R-TreeSearch
# Automatically generated by CRAN2OBS
#
# Spec file for package TreeSearch
# This file is auto-generated using information in the package source,
# esp. Description and Summary. Improvements in that area should be
# discussed with upstream.
#
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# published by the Open Source Initiative.
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%global packname TreeSearch
%global rlibdir %{_libdir}/R/library
Name: R-%{packname}
Version: 1.7.0
Release: 0
Summary: Phylogenetic Analysis with Discrete Character Data
Group: Development/Libraries/Other
License: GPL (>= 3)
URL: http://cran.r-project.org/web/packages/%{packname}
Source: TreeSearch_1.7.0.tar.gz
Requires: R-base
Requires: R-ape
Requires: R-cli
Requires: R-fastmap
Requires: R-fastmatch
Requires: R-fs
Requires: R-future
Requires: R-PlotTools
Requires: R-promises
Requires: R-protoclust
Requires: R-Rcpp
Requires: R-Rdpack
Requires: R-Rogue
Requires: R-shiny
Requires: R-shinyjs
Requires: R-stringi
Requires: R-TreeDist
Requires: R-TreeTools
Requires: R-digest
Requires: R-globals
Requires: R-listenv
Requires: R-parallelly
Requires: R-later
Requires: R-lifecycle
Requires: R-magrittr
Requires: R-otel
Requires: R-R6
Requires: R-rlang
Requires: R-rbibutils
Requires: R-matrixStats
Requires: R-Rfast
Requires: R-bslib
Requires: R-cachem
Requires: R-commonmark
Requires: R-fontawesome
Requires: R-glue
Requires: R-htmltools
Requires: R-httpuv
Requires: R-jsonlite
Requires: R-mime
Requires: R-sourcetools
Requires: R-withr
Requires: R-xtable
Requires: R-colorspace
Requires: R-bit64
Requires: R-RCurl
Requires: R-bit
Requires: R-base64enc
Requires: R-jquerylib
Requires: R-memoise
Requires: R-sass
Requires: R-bitops
Requires: R-zigg
Requires: R-RcppParallel
Requires: R-RcppArmadillo
Requires: R-rappdirs
# %%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-ape
BuildRequires: R-cli
BuildRequires: R-fastmap
BuildRequires: R-fastmatch
BuildRequires: R-fs
BuildRequires: R-future
BuildRequires: R-PlotTools
BuildRequires: R-promises
BuildRequires: R-protoclust
BuildRequires: R-Rcpp-devel
BuildRequires: R-Rdpack
BuildRequires: R-Rogue
BuildRequires: R-shiny
BuildRequires: R-shinyjs
BuildRequires: R-stringi
BuildRequires: R-TreeDist
BuildRequires: R-TreeTools
BuildRequires: R-digest
BuildRequires: R-globals
BuildRequires: R-listenv
BuildRequires: R-parallelly
BuildRequires: R-later
BuildRequires: R-lifecycle
BuildRequires: R-magrittr
BuildRequires: R-otel
BuildRequires: R-R6
BuildRequires: R-rlang
BuildRequires: R-rbibutils
BuildRequires: R-matrixStats
BuildRequires: R-Rfast
BuildRequires: R-bslib
BuildRequires: R-cachem
BuildRequires: R-commonmark
BuildRequires: R-fontawesome
BuildRequires: R-glue
BuildRequires: R-htmltools
BuildRequires: R-httpuv
BuildRequires: R-jsonlite
BuildRequires: R-mime
BuildRequires: R-sourcetools-devel
BuildRequires: R-withr
BuildRequires: R-xtable
BuildRequires: R-colorspace
BuildRequires: R-bit64
BuildRequires: R-RCurl
BuildRequires: R-bit
BuildRequires: R-base64enc
BuildRequires: R-jquerylib
BuildRequires: R-memoise
BuildRequires: R-sass
BuildRequires: R-bitops
BuildRequires: R-zigg
BuildRequires: R-RcppParallel-devel
BuildRequires: R-RcppArmadillo-devel
BuildRequires: R-rappdirs
BuildRequires: gcc gcc-c++ gcc-fortran
Suggests: R-knitr
Suggests: R-phangorn
Suggests: R-Quartet
Suggests: R-readxl
Suggests: R-rmarkdown
Suggests: R-shinytest
Suggests: R-spelling
Suggests: R-testthat
Suggests: R-vdiffr
%description
Reconstruct phylogenetic trees from discrete data. Inapplicable
character states are handled using the algorithm of Brazeau, Guillerme
and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy" library,
under equal or implied step weights. Contains a "shiny" user interface
for interactive tree search and exploration of results, including
character visualization, rogue taxon detection, tree space mapping, and
cluster consensus trees (Smith 2022a, b) <doi:10.1093/sysbio/syab099>,
<doi:10.1093/sysbio/syab100>. Profile Parsimony (Faith and Trueman,
2001) <doi:10.1080/10635150118627>, Successive Approximations (Farris,
1969) <doi:10.2307/2412182> and custom optimality criteria are
implemented.
%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}/Parsimony
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/REFERENCES.bib
%{rlibdir}/%{packname}/WORDLIST
%{rlibdir}/%{packname}/apa-old-doi-prefix.csl
%{rlibdir}/%{packname}/data
%{rlibdir}/%{packname}/datasets
%{rlibdir}/%{packname}/doc
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%{rlibdir}/%{packname}/libs
%{rlibdir}/%{packname}/preamble.tex
%{rlibdir}/%{packname}/tests
%changelog
