File R-ontophylo.spec of Package R-ontophylo
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# Spec file for package ontophylo
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%global packname ontophylo
%global rlibdir %{_libdir}/R/library
Name: R-%{packname}
Version: 1.1.3
Release: 0
Summary: Ontology-Informed Phylogenetic Comparative Analyses
Group: Development/Libraries/Other
License: MIT + file LICENSE
URL: http://cran.r-project.org/web/packages/%{packname}
Source: ontophylo_1.1.3.tar.gz
Requires: R-base
Requires: R-magrittr
Requires: R-dplyr
Requires: R-tidyr
Requires: R-purrr
Requires: R-tibble
Requires: R-ggplot2
Requires: R-stringdist
Requires: R-ape
Requires: R-phytools
Requires: R-ontologyIndex
Requires: R-RColorBrewer
Requires: R-truncnorm
Requires: R-fANCOVA
Requires: R-grImport
Requires: R-Rcpp
Requires: R-digest
Requires: R-cli
Requires: R-generics
Requires: R-glue
Requires: R-lifecycle
Requires: R-pillar
Requires: R-R6
Requires: R-rlang
Requires: R-tidyselect
Requires: R-vctrs
Requires: R-gtable
Requires: R-isoband
Requires: R-S7
Requires: R-scales
Requires: R-withr
Requires: R-XML
Requires: R-maps
Requires: R-clusterGeneration
Requires: R-coda
Requires: R-combinat
Requires: R-DEoptim
Requires: R-doParallel
Requires: R-expm
Requires: R-foreach
Requires: R-mnormt
Requires: R-numDeriv
Requires: R-optimParallel
Requires: R-phangorn
Requires: R-scatterplot3d
Requires: R-pkgconfig
Requires: R-stringr
Requires: R-cpp11
Requires: R-iterators
Requires: R-fastmatch
Requires: R-igraph
Requires: R-quadprog
Requires: R-utf8
Requires: R-farver
Requires: R-labeling
Requires: R-viridisLite
Requires: R-stringi
# %%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
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# %endif
# BuildRequires: texinfo
BuildRequires: fdupes
BuildRequires: R-base
BuildRequires: R-magrittr
BuildRequires: R-dplyr
BuildRequires: R-tidyr
BuildRequires: R-purrr
BuildRequires: R-tibble
BuildRequires: R-ggplot2
BuildRequires: R-stringdist
BuildRequires: R-ape
BuildRequires: R-phytools
BuildRequires: R-ontologyIndex
BuildRequires: R-RColorBrewer
BuildRequires: R-truncnorm
BuildRequires: R-fANCOVA
BuildRequires: R-grImport
BuildRequires: R-Rcpp-devel
BuildRequires: R-digest
BuildRequires: R-cli
BuildRequires: R-generics
BuildRequires: R-glue
BuildRequires: R-lifecycle
BuildRequires: R-pillar
BuildRequires: R-R6
BuildRequires: R-rlang
BuildRequires: R-tidyselect
BuildRequires: R-vctrs
BuildRequires: R-gtable
BuildRequires: R-isoband
BuildRequires: R-S7
BuildRequires: R-scales
BuildRequires: R-withr
BuildRequires: R-XML
BuildRequires: R-maps
BuildRequires: R-clusterGeneration
BuildRequires: R-coda
BuildRequires: R-combinat
BuildRequires: R-DEoptim
BuildRequires: R-doParallel
BuildRequires: R-expm
BuildRequires: R-foreach
BuildRequires: R-mnormt
BuildRequires: R-numDeriv
BuildRequires: R-optimParallel
BuildRequires: R-phangorn
BuildRequires: R-scatterplot3d
BuildRequires: R-pkgconfig
BuildRequires: R-stringr
BuildRequires: R-cpp11-devel
BuildRequires: R-iterators
BuildRequires: R-fastmatch
BuildRequires: R-igraph
BuildRequires: R-quadprog
BuildRequires: R-utf8
BuildRequires: R-farver
BuildRequires: R-labeling
BuildRequires: R-viridisLite
BuildRequires: R-stringi
Suggests: R-rmarkdown
Suggests: R-knitr
Suggests: R-roxygen2
Suggests: R-testthat
Suggests: R-stringr
%description
Provides new tools for analyzing discrete trait data integrating
bio-ontologies and phylogenetics. It expands on the previous work of
Tarasov et al. (2019) <doi:10.1093/isd/ixz009>. The PARAMO pipeline
allows to reconstruct ancestral phenomes treating groups of
morphological traits as a single complex character. The pipeline
incorporates knowledge from ontologies during the amalgamation of
individual character stochastic maps. Here we expand the current PARAMO
functionality by adding new statistical methods for inferring
evolutionary phenome dynamics using non-homogeneous Poisson process
(NHPP). The new functionalities include: (1) reconstruction of
evolutionary rate shifts of phenomes across lineages and time; (2)
reconstruction of morphospace dynamics through time; and (3) estimation
of rates of phenome evolution at different levels of anatomical
hierarchy (e.g., entire body or specific regions only). The package
also includes user-friendly tools for visualizing evolutionary rates of
different anatomical regions using vector images of the organisms of
interest.
%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
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/data
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%changelog
