automatic import of R-CRAN-treebalancef40

3 files changed, 85 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..14fa6f1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1 @@
+/treebalance_1.2.0.tar.gz
diff --git a/R-CRAN-treebalance.spec b/R-CRAN-treebalance.spec
new file mode 100644
index 0000000..681cc5e
--- /dev/null
+++ b/R-CRAN-treebalance.spec
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+%global __brp_check_rpaths %{nil}
+%global __requires_exclude ^libmpi
+%global packname  treebalance
+%global packver   1.2.0
+%global rlibdir   /usr/local/lib/R/library
+
+Name:             R-CRAN-%{packname}
+Version:          1.2.0
+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 
+BuildRequires:    R-CRAN-gmp 
+Requires:         R-CRAN-ape 
+Requires:         R-CRAN-memoise 
+Requires:         R-CRAN-gmp 
+
+%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 book ''Tree balance indices: a comprehensive
+survey'' by M. Fischer, L. Herbst, S. Kersting, L. Kuehn and K. Wicke
+(2023) <ISBN: 978-3-031-39799-8>, <doi:10.1007/978-3-031-39800-1>, which
+gives a precise definition for the terms 'balance index' and 'imbalance
+index' (Chapter 4) and provides an overview of the terminology in this
+manual (Chapter 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 and index families: 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 9 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 total
+internal path length, the total path length, the average vertex depth, the
+maximum width, the modified maximum difference in widths, the maximum
+depth, the maximum width over maximum 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..fd22154
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+5a3a15e26ac27d24cf0c681b4654d18a  treebalance_1.2.0.tar.gz