New upstream version 1.57 (291de8a8) · Commits · Debian Med / cluster3

ChangeLog

+8 −0

Original line number	Diff line number	Diff line
		2018.11.22
		Fixed memory leaks in kcluster and treecluster in src/cluster.c, and in
		Hierarchical and KMeans in src/command.c; these memory leaks occurred when
		memory allocation failed.
		Fixed a bug in the distancematrix function Bio/Cluster/__init__.py, where the
		weight argument was not properly initialized if it had the default value None,
		causing the function to fail.

		2018.04.29
		In the Python wrapper python/clustermodule.c, use PyTree_new to initialize Tree
		objects instead of PyTree_init, as Tree objects are immutable. Check if the

NEWS

+7 −13

Original line number	Diff line number	Diff line
		2018.04.29
		In the Python wrapper python/clustermodule.c, use PyTree_new to initialize Tree
		objects instead of PyTree_init, as Tree objects are immutable. Check if the
		argument passed are nodes by using PyType_IsSubtype instead of comparing against
		PyNodeType directly, as Node in __init__.py is a subtype of Node in
		clustermodule.c.
		Rewrote indexing code for PyTree for Python3.
		Fixed a bug in Tree.cut in Bio/Cluster/__init__.py, which calculated the indices
		but did not return them. Updated the documentation for Tree.cut and Tree.sort
		in Bio/Cluster/__init__.py. Added tests for Tree.cut. Updated the documentation
		for Pycluster.
		Fixed a bug in src/cluster.c where a NULL pointer was freed if memory
		allocation failed.
		2018.11.22
		Fixed memory leaks in kcluster and treecluster in src/cluster.c, and in
		Hierarchical and KMeans in src/command.c; these memory leaks occurred when
		memory allocation failed.
		Fixed a bug in the distancematrix function Bio/Cluster/__init__.py, where the
		weight argument was not properly initialized if it had the default value None,
		causing the function to fail.

configure

+10 −10

Original line number	Diff line number	Diff line
		#! /bin/sh
		# Guess values for system-dependent variables and create Makefiles.
		# Generated by GNU Autoconf 2.69 for cluster 1.56.
		# Generated by GNU Autoconf 2.69 for cluster 1.57.
		#
		#
		# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
		@@ -577,8 +577,8 @@ MAKEFLAGS=
		# Identity of this package.
		PACKAGE_NAME='cluster'
		PACKAGE_TARNAME='cluster'
		PACKAGE_VERSION='1.56'
		PACKAGE_STRING='cluster 1.56'
		PACKAGE_VERSION='1.57'
		PACKAGE_STRING='cluster 1.57'
		PACKAGE_BUGREPORT=''
		PACKAGE_URL=''

		@@ -1273,7 +1273,7 @@ if test "$ac_init_help" = "long"; then
		# Omit some internal or obsolete options to make the list less imposing.
		# This message is too long to be a string in the A/UX 3.1 sh.
		cat <<_ACEOF
		\`configure' configures cluster 1.56 to adapt to many kinds of systems.
		\`configure' configures cluster 1.57 to adapt to many kinds of systems.

		Usage: $0 [OPTION]... [VAR=VALUE]...

		@@ -1343,7 +1343,7 @@ fi

		if test -n "$ac_init_help"; then
		case $ac_init_help in
		short \| recursive ) echo "Configuration of cluster 1.56:";;
		short \| recursive ) echo "Configuration of cluster 1.57:";;
		esac
		cat <<\_ACEOF

		@@ -1440,7 +1440,7 @@ fi
		test -n "$ac_init_help" && exit $ac_status
		if $ac_init_version; then
		cat <<\_ACEOF
		cluster configure 1.56
		cluster configure 1.57
		generated by GNU Autoconf 2.69

		Copyright (C) 2012 Free Software Foundation, Inc.
		@@ -1859,7 +1859,7 @@ cat >config.log <<_ACEOF
		This file contains any messages produced by compilers while
		running configure, to aid debugging if configure makes a mistake.

		It was created by cluster $as_me 1.56, which was
		It was created by cluster $as_me 1.57, which was
		generated by GNU Autoconf 2.69. Invocation command line was

		$ $0 $@
		@@ -2723,7 +2723,7 @@ fi

		# Define the identity of the package.
		PACKAGE='cluster'
		VERSION='1.56'
		VERSION='1.57'


		cat >>confdefs.h <<_ACEOF
		@@ -6009,7 +6009,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF \|\| ac_write_fail=1
		# report actual input values of CONFIG_FILES etc. instead of their
		# values after options handling.
		ac_log="
		This file was extended by cluster $as_me 1.56, which was
		This file was extended by cluster $as_me 1.57, which was
		generated by GNU Autoconf 2.69. Invocation command line was

		CONFIG_FILES = $CONFIG_FILES
		@@ -6075,7 +6075,7 @@ _ACEOF
		cat >>$CONFIG_STATUS <<_ACEOF \|\| ac_write_fail=1
		ac_cs_config="`$as_echo "$ac_configure_args" \| sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
		ac_cs_version="\\
		cluster config.status 1.56
		cluster config.status 1.57
		configured by $0, generated by GNU Autoconf 2.69,
		with options \\"\$ac_cs_config\\"

configure.ac

+1 −1

Original line number	Diff line number	Diff line
		# Process this file with autoconf to produce a configure script.
		AC_INIT(cluster, 1.56)
		AC_INIT(cluster, 1.57)
		AC_CONFIG_SRCDIR(src/cluster.c)
		AM_INIT_AUTOMAKE
		AC_CONFIG_HEADERS(config.h)

doc/cluster.pdf

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