automatic import of R-CRAN-treebalance

3 files changed, 79 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..9c43294 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1 @@
+/treebalance_1.1.0.tar.gz
diff --git a/R-CRAN-treebalance.spec b/R-CRAN-treebalance.spec
new file mode 100644
index 0000000..966fe98
--- /dev/null
+++ b/R-CRAN-treebalance.spec
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+%global __brp_check_rpaths %{nil}
+%global packname  treebalance
+%global packver   1.1.0
+%global rlibdir   /usr/local/lib/R/library
+
+Name:             R-CRAN-%{packname}
+Version:          1.1.0
+Release:          1%{?dist}%{?buildtag}
+Summary:          Computation of Tree (Im)Balance Indices
+
+License:          GPL-3
+URL:              https://cran.r-project.org/package=%{packname}
+Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz
+
+
+BuildRequires:    R-devel >= 3.5.0
+Requires:         R-core >= 3.5.0
+BuildArch:        noarch
+BuildRequires:    R-CRAN-ape 
+BuildRequires:    R-CRAN-memoise 
+Requires:         R-CRAN-ape 
+Requires:         R-CRAN-memoise 
+
+%description
+The aim of the 'R' package 'treebalance' is to provide functions for the
+computation of a large variety of (im)balance indices for rooted trees.
+The package accompanies the manuscript ''Tree balance indices: a
+comprehensive survey'' by M. Fischer, L. Herbst, S. Kersting, L. Kuehn and
+K. Wicke (2021) <arXiv:2109.12281>, which gives a precise definition for
+the terms 'balance index' and 'imbalance index' (Section 3) and provides
+an overview of the terminology in this manual (Section 2). For further
+information on (im)balance indices, see also Fischer et al. (2021)
+<https://treebalance.wordpress.com>. Considering both established and new
+(im)balance indices, 'treebalance' provides (among others) functions for
+calculating the following 18 established indices: the average leaf depth,
+the B1 and B2 index, the Colijn-Plazzotta rank, the normal, corrected,
+quadratic and equal weights Colless index, the family of Colless-like
+indices, the family of I-based indices, the Rogers J index, the Furnas
+rank, the rooted quartet index, the s-shape statistic, the Sackin index,
+the symmetry nodes index, the total cophenetic index and the variance of
+leaf depths. Additionally, we include 5 tree shape statistics that satisfy
+the definition of an (im)balance index but have not been thoroughly
+analyzed in terms of tree balance in the literature yet. These are: the
+maximum width, the maximum difference in widths, the maximal depth, the
+stairs1 and the stairs2 index. As input, most functions of 'treebalance'
+require a rooted (phylogenetic) tree in 'phylo' format (as introduced in
+'ape' 1.9 in November 2006). 'phylo' is used to store (phylogenetic) trees
+with no vertices of out-degree one. For further information on the format
+we kindly refer the reader to E. Paradis (2012)
+<http://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.pdf>.
+
+%prep
+%setup -q -c -n %{packname}
+
+# fix end of executable files
+find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \;
+# prevent binary stripping
+[ -d %{packname}/src ] && find %{packname}/src -type f -exec \
+  sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true
+[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \
+  sed -i 's@-g0@@g' {} \; || true
+# don't allow local prefix in executable scripts
+find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \;
+
+%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
+# remove buildroot from installed files
+find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \;
+
+%files
+%{rlibdir}/%{packname}
diff --git a/sources b/sources
new file mode 100644
index 0000000..7bd9695
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+a59fa4b04b2ce7422fe8fde741175c8c  treebalance_1.1.0.tar.gz