File R-HACSim.spec of Package R-HACSim

# Automatically generated by CRAN2OBS
# 
# Spec file for package HACSim 
# 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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%global packname  HACSim 
%global rlibdir   %{_libdir}/R/library 
 
Name:           R-%{packname} 
Version:        1.0.7.1 
Release:        0 
Summary:        Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment 
Group:          Development/Libraries/Other 
License:        GPL-3 
URL:            http://cran.r-project.org/web/packages/%{packname} 
Source:         HACSim_1.0.7-1.tar.gz 
Requires:       R-base 
Requires:	R-ape
Requires:	R-data.table
Requires:	R-matrixStats
Requires:	R-pegas
Requires:	R-Rcpp
Requires:	R-stringr
Requires:	R-RcppArmadillo
Requires:	R-digest
Requires:	R-cli
Requires:	R-glue
Requires:	R-lifecycle
Requires:	R-magrittr
Requires:	R-rlang
Requires:	R-stringi
Requires:	R-vctrs
 
# %%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-data.table
BuildRequires: 	R-matrixStats
BuildRequires: 	R-pegas
BuildRequires: 	R-Rcpp-devel
BuildRequires: 	R-stringr
BuildRequires: 	R-RcppArmadillo-devel
BuildRequires: 	R-digest
BuildRequires: 	R-cli
BuildRequires: 	R-glue
BuildRequires: 	R-lifecycle
BuildRequires: 	R-magrittr
BuildRequires: 	R-rlang
BuildRequires: 	R-stringi
BuildRequires: 	R-vctrs
BuildRequires:  gcc gcc-c++ gcc-fortran
 
%description 
Performs iterative extrapolation of species' haplotype accumulation 
curves using a nonparametric stochastic (Monte Carlo) optimization 
method for assessment of specimen sampling completeness based on the 
approach of Phillips et al. (2015) <doi:10.1515/dna-2015-0008>, 
Phillips et al. (2019) <doi:10.1002/ece3.4757> and Phillips et al. 
(2020) <doi: 10.7717/peerj-cs.243>. 'HACSim' outputs a number of useful 
summary statistics of sampling coverage ("Measures of Sampling 
Closeness"), including an estimate of the likely required sample size 
(along with desired level confidence intervals) necessary to recover a 
given number/proportion of observed unique species' haplotypes. Any 
genomic marker can be targeted to assess likely required specimen 
sample sizes for genetic diversity assessment. The method is 
particularly well-suited to assess sampling sufficiency for DNA 
barcoding initiatives. Users can also simulate their own DNA sequences 
according to various models of nucleotide substitution. A Shiny app is 
also available. 
 
%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
%{rlibdir}/%{packname}/R
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%{rlibdir}/%{packname}/libs
 
%changelog