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AUTHORS
View file @ 881bc15b
Michiel de Hoon (currently at the RIKEN Center for Life Science Technologies),
Michiel de Hoon
(currently at the RIKEN Center for Integrative Medical Sciences),
SunYong Kim, Seiya Imoto, and Satoru Miyano.
University of Tokyo,
......
ChangeLog
View file @ 881bc15b
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.
2018.04.14
The calculation of the Spearman correlation and Kendall's tau now take the
values of the weight array into account (previously, the weights were ignored
for the Spearman correlation and Kendall's tau).
Let cuttree in the C Clustering Library return an int to be able to indicate
memory allocation problems.
The distancematrix function in the C Clustering Library now requires storage
for the distance matrix to be allocated before calling distancematrix.
The Python wrappers python/clustermodule.c, python/__init__.py were rewritten
to allow compilation without requiring numpy; numpy is needed at runtime only.
2017.09.23
Fixed the kmedoids function, which may count the number of solutions
incorrectly (and report an error message) if the initial clustering is given by the user.
Using the C11-standard definition of "int main", where argv is not a const char* array.
Save the Interface Builder files for the Mac version in XIB format.
Update Controller.m in the Mac version to avoid warnings converting Objective-C
strings to plain C strings.
2017.08.19
Include Michael Eisen's original demo.txt example data in the distribution.
For k-means clustering, show the number of solutions found separately for genes
......
INSTALL
View file @ 881bc15b
......@@ -86,15 +86,17 @@ Python
In the top directory (containing setup.py and also this INSTALL file), type
python setup.py install
You will need a fairly recent version of Python (2.0 or higher) and the
Numerical Python package (NumPy version 1.1.1 or later), as well as an ANSI C
compiler such as GNU gcc. You may need to log in as root the install Pycluster.
You will need a fairly recent version of Python (2.6 or higher), as well as
an ANSI C compiler such as GNU gcc.
You may need to log in as root the install Pycluster.
If you do not have root access, do
python setup.py install --prefix=/some/other/directory
and set the environment variable
PYTHONPATH=/some/other/directory/lib/python2.2/site-packages
The exact command depends on which shell you are using; the exact path will
depend on the version of Python you are using.
To use Pycluster, you will also need numpy (Numerical Python). Pycluster was
tested with numpy version 1.7.0; older versions may also work.
Note that Pycluster is also available as a tarball containing only the source
code needed for Pycluster. A Windows installer for Pycluster is available from
......@@ -124,5 +126,5 @@ CONTACT
=======
Michiel de Hoon, University of Tokyo, Human Genome Center
(currently at the RIKEN Center for Life Science Technologies)
(currently at the RIKEN Center for Integrative Medical Sciences).
Email: michiel.dehoon 'AT' riken.jp
Makefile.am
View file @ 881bc15b
......@@ -7,12 +7,9 @@ WINDIST = windows/cluster.hhp windows/cluster.ico windows/cluster.iss \
windows/resources.h windows/resources.rc
MACDIST = mac/main.m mac/Controller.h mac/Controller.m mac/cluster.icns \
mac/English.lproj/InfoPlist.strings \
mac/English.lproj/AboutPanel.nib/designable.nib \
mac/English.lproj/AboutPanel.nib/keyedobjects.nib \
mac/English.lproj/FileFormatPanel.nib/designable.nib \
mac/English.lproj/FileFormatPanel.nib/keyedobjects.nib \
mac/English.lproj/MainMenu.nib/designable.nib \
mac/English.lproj/MainMenu.nib/keyedobjects.nib \
mac/English.lproj/AboutPanel.xib \
mac/English.lproj/FileFormatPanel.xib \
mac/English.lproj/MainMenu.xib \
mac/Cluster.xcodeproj/project.pbxproj mac/Makefile mac/Info.plist
PYTHONDIST = setup.py python/MANIFEST.python python/__init__.py \
python/clustermodule.c python/test/README python/test/test_Cluster.py
......@@ -28,7 +25,7 @@ PERLDIST = perl/Artistic.txt perl/MANIFEST.perl \
perl/examples/ex5_treecluster perl/examples/ex6_clusterdistance \
perl/examples/ex7_distancematrix perl/examples/ex8_kmedoids
EXAMPLEDIST = example/example.c example/Makefile example/README
HTMLDIST = html/mac.py html/Makefile
HTMLDIST = html/mac.py html/windows.py html/Makefile
DATADIST = data/README data/cyano.txt data/demo.txt
......
Makefile.in
View file @ 881bc15b
# Makefile.in generated by automake 1.14 from Makefile.am.
# Makefile.in generated by automake 1.16.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
# Copyright (C) 1994-2018 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -14,7 +14,17 @@
@SET_MAKE@
VPATH = @srcdir@
am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
am__is_gnu_make = { \
if test -z '$(MAKELEVEL)'; then \
false; \
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true; \
elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
true; \
else \
false; \
fi; \
}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
......@@ -76,15 +86,12 @@ NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
subdir = .
DIST_COMMON = INSTALL NEWS README AUTHORS ChangeLog \
$(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/configure $(am__configure_deps) \
$(srcdir)/config.h.in COPYING TODO compile depcomp install-sh \
missing
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
DIST_COMMON = $(srcdir)/Makefile.am $(top_srcdir)/configure \
$(am__configure_deps) $(am__DIST_COMMON)
am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
configure.lineno config.status.lineno
mkinstalldirs = $(install_sh) -d
......@@ -125,7 +132,7 @@ am__recursive_targets = \
$(RECURSIVE_CLEAN_TARGETS) \
$(am__extra_recursive_targets)
AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
cscope distdir dist dist-all distcheck
cscope distdir distdir-am dist dist-all distcheck
am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) \
$(LISP)config.h.in
# Read a list of newline-separated strings from the standard input,
......@@ -148,6 +155,9 @@ ETAGS = etags
CTAGS = ctags
CSCOPE = cscope
DIST_SUBDIRS = X11 src
am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/config.h.in AUTHORS \
COPYING ChangeLog INSTALL NEWS README TODO compile depcomp \
install-sh missing
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
distdir = $(PACKAGE)-$(VERSION)
top_distdir = $(distdir)
......@@ -292,12 +302,9 @@ WINDIST = windows/cluster.hhp windows/cluster.ico windows/cluster.iss \
MACDIST = mac/main.m mac/Controller.h mac/Controller.m mac/cluster.icns \
mac/English.lproj/InfoPlist.strings \
mac/English.lproj/AboutPanel.nib/designable.nib \
mac/English.lproj/AboutPanel.nib/keyedobjects.nib \
mac/English.lproj/FileFormatPanel.nib/designable.nib \
mac/English.lproj/FileFormatPanel.nib/keyedobjects.nib \
mac/English.lproj/MainMenu.nib/designable.nib \
mac/English.lproj/MainMenu.nib/keyedobjects.nib \
mac/English.lproj/AboutPanel.xib \
mac/English.lproj/FileFormatPanel.xib \
mac/English.lproj/MainMenu.xib \
mac/Cluster.xcodeproj/project.pbxproj mac/Makefile mac/Info.plist
PYTHONDIST = setup.py python/MANIFEST.python python/__init__.py \
......@@ -316,7 +323,7 @@ PERLDIST = perl/Artistic.txt perl/MANIFEST.perl \
perl/examples/ex7_distancematrix perl/examples/ex8_kmedoids
EXAMPLEDIST = example/example.c example/Makefile example/README
HTMLDIST = html/mac.py html/Makefile
HTMLDIST = html/mac.py html/windows.py html/Makefile
DATADIST = data/README data/cyano.txt data/demo.txt
@MOTIF_TRUE@MAYBE_X11 = X11
SUBDIRS = $(MAYBE_X11) src
......@@ -342,15 +349,14 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
echo ' $(SHELL) ./config.status'; \
$(SHELL) ./config.status;; \
*) \
echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \
cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \
echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__maybe_remake_depfiles)'; \
cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__maybe_remake_depfiles);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
......@@ -483,7 +489,10 @@ distclean-tags:
-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-rm -f cscope.out cscope.in.out cscope.po.out cscope.files
distdir: $(DISTFILES)
distdir: $(BUILT_SOURCES)
$(MAKE) $(AM_MAKEFLAGS) distdir-am
distdir-am: $(DISTFILES)
$(am__remove_distdir)
test -d "$(distdir)" || mkdir "$(distdir)"
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
......@@ -548,7 +557,7 @@ distdir: $(DISTFILES)
! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
|| chmod -R a+r "$(distdir)"
dist-gzip: distdir
tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
tardir=$(distdir) && $(am__tar) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).tar.gz
$(am__post_remove_distdir)
dist-bzip2: distdir
......@@ -564,17 +573,17 @@ dist-xz: distdir
$(am__post_remove_distdir)
dist-tarZ: distdir
@echo WARNING: "Support for shar distribution archives is" \
"deprecated." >&2
@echo WARNING: "Support for distribution archives compressed with" \
"legacy program 'compress' is deprecated." >&2
@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
$(am__post_remove_distdir)
dist-shar: distdir
@echo WARNING: "Support for distribution archives compressed with" \
"legacy program 'compress' is deprecated." >&2
@echo WARNING: "Support for shar distribution archives is" \
"deprecated." >&2
@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
shar $(distdir) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).shar.gz
$(am__post_remove_distdir)
dist-zip: distdir
......@@ -592,7 +601,7 @@ dist dist-all:
distcheck: dist
case '$(DIST_ARCHIVES)' in \
*.tar.gz*) \
GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).tar.gz | $(am__untar) ;;\
*.tar.bz2*) \
bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
*.tar.lz*) \
......@@ -602,22 +611,23 @@ distcheck: dist
*.tar.Z*) \
uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
*.shar.gz*) \
GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\
*.zip*) \
unzip $(distdir).zip ;;\
esac
chmod -R a-w $(distdir)
chmod u+w $(distdir)
mkdir $(distdir)/_build $(distdir)/_inst
mkdir $(distdir)/_build $(distdir)/_build/sub $(distdir)/_inst
chmod a-w $(distdir)
test -d $(distdir)/_build || exit 0; \
dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
&& dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
&& am__cwd=`pwd` \
&& $(am__cd) $(distdir)/_build \
&& ../configure --srcdir=.. --prefix="$$dc_install_base" \
&& $(am__cd) $(distdir)/_build/sub \
&& ../../configure \
$(AM_DISTCHECK_CONFIGURE_FLAGS) \
$(DISTCHECK_CONFIGURE_FLAGS) \
--srcdir=../.. --prefix="$$dc_install_base" \
&& $(MAKE) $(AM_MAKEFLAGS) \
&& $(MAKE) $(AM_MAKEFLAGS) dvi \
&& $(MAKE) $(AM_MAKEFLAGS) check \
......@@ -792,6 +802,8 @@ uninstall-am:
mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
uninstall-am
.PRECIOUS: Makefile
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
......
NEWS
View file @ 881bc15b
2017.08.19
Include Michael Eisen's original demo.txt example data in the distribution.
For k-means clustering, show the number of solutions found separately for genes
and arrays.
Let cuttree number the clusters incrementally in the left-to-right order of
the leaves in the hierarchical clustering tree.
Algorithm::Cluster::cuttree now returns an array.
Removed mean, median from the Python tests.
Updates for Unicode handling in Python3.
Fix slice bug in Pycluster's Tree class.
Write a new function sorttree that reorders a hierarchical clustering tree
such that the nodes are ordered according to a user-specified order, while
maintaining the structure of the hierarchical clustering tree. The sorttree
function is used in the HierarchicalCluster function, and can also be called
from Pycluster and from Algorithm::Cluster.
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.
README
View file @ 881bc15b
......@@ -63,6 +63,5 @@ CONTACT
Michiel de Hoon
University of Tokyo, Institute of Medical Science
Human Genome Center, Laboratory of DNA Information Analysis
Currently at
RIKEN Center for Life Science Technologies
Currently at the RIKEN Center for Integrative Medical Sciences.
michiel.dehoon 'AT' riken.jp
X11/Makefile.in
View file @ 881bc15b
# Makefile.in generated by automake 1.14 from Makefile.am.
# Makefile.in generated by automake 1.16.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
# Copyright (C) 1994-2018 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -16,7 +16,17 @@
VPATH = @srcdir@
am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
am__is_gnu_make = { \
if test -z '$(MAKELEVEL)'; then \
false; \
elif test -n '$(MAKE_HOST)'; then \
true; \
elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
true; \
else \
false; \
fi; \
}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
......@@ -78,13 +88,13 @@ NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
subdir = X11
DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp $(dist_doc_DATA) $(dist_fileformat_DATA) \
$(dist_html_DATA) $(dist_image_DATA)
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
DIST_COMMON = $(srcdir)/Makefile.am $(dist_doc_DATA) \
$(dist_fileformat_DATA) $(dist_html_DATA) $(dist_image_DATA) \
$(am__DIST_COMMON)
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config.h
CONFIG_CLEAN_FILES =
......@@ -114,7 +124,8 @@ am__v_at_0 = @
am__v_at_1 =
DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__maybe_remake_depfiles = depfiles
am__depfiles_remade = ./$(DEPDIR)/gui.Po
am__mv = mv -f
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
......@@ -185,6 +196,7 @@ am__define_uniq_tagged_files = \
done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
am__DIST_COMMON = $(srcdir)/Makefile.in $(top_srcdir)/depcomp
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
......@@ -308,14 +320,13 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu X11/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu X11/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
......@@ -341,7 +352,13 @@ mostlyclean-compile:
distclean-compile:
-rm -f *.tab.c
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gui.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gui.Po@am__quote@ # am--include-marker
$(am__depfiles_remade):
@$(MKDIR_P) $(@D)
@echo '# dummy' >$@-t && $(am__mv) $@-t $@
am--depfiles: $(am__depfiles_remade)
.c.o:
@am__fastdepCC_TRUE@ $(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
......@@ -493,7 +510,10 @@ cscopelist-am: $(am__tagged_files)
distclean-tags:
-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
distdir: $(DISTFILES)
distdir: $(BUILT_SOURCES)
$(MAKE) $(AM_MAKEFLAGS) distdir-am
distdir-am: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
......@@ -565,7 +585,7 @@ clean: clean-am
clean-am: clean-generic clean-noinstLIBRARIES mostlyclean-am
distclean: distclean-am
-rm -rf ./$(DEPDIR)
-rm -f ./$(DEPDIR)/gui.Po
-rm -f Makefile
distclean-am: clean-am distclean-compile distclean-generic \
distclean-tags
......@@ -612,7 +632,7 @@ install-ps-am:
installcheck-am:
maintainer-clean: maintainer-clean-am
-rm -rf ./$(DEPDIR)
-rm -f ./$(DEPDIR)/gui.Po
-rm -f Makefile
maintainer-clean-am: distclean-am maintainer-clean-generic
......@@ -633,23 +653,25 @@ uninstall-am: uninstall-dist_docDATA uninstall-dist_fileformatDATA \
.MAKE: install-am install-strip
.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \
clean-noinstLIBRARIES cscopelist-am ctags ctags-am distclean \
distclean-compile distclean-generic distclean-tags distdir dvi \
dvi-am html html-am info info-am install install-am \
install-data install-data-am install-dist_docDATA \
install-dist_fileformatDATA install-dist_htmlDATA \
install-dist_imageDATA install-dvi install-dvi-am install-exec \
install-exec-am install-html install-html-am install-info \
install-info-am install-man install-pdf install-pdf-am \
install-ps install-ps-am install-strip installcheck \
installcheck-am installdirs maintainer-clean \
maintainer-clean-generic mostlyclean mostlyclean-compile \
mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
uninstall-am uninstall-dist_docDATA \
.PHONY: CTAGS GTAGS TAGS all all-am am--depfiles check check-am clean \
clean-generic clean-noinstLIBRARIES cscopelist-am ctags \
ctags-am distclean distclean-compile distclean-generic \
distclean-tags distdir dvi dvi-am html html-am info info-am \
install install-am install-data install-data-am \
install-dist_docDATA install-dist_fileformatDATA \
install-dist_htmlDATA install-dist_imageDATA install-dvi \
install-dvi-am install-exec install-exec-am install-html \
install-html-am install-info install-info-am install-man \
install-pdf install-pdf-am install-ps install-ps-am \
install-strip installcheck installcheck-am installdirs \
maintainer-clean maintainer-clean-generic mostlyclean \
mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
tags tags-am uninstall uninstall-am uninstall-dist_docDATA \
uninstall-dist_fileformatDATA uninstall-dist_htmlDATA \
uninstall-dist_imageDATA
.PRECIOUS: Makefile
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
......
aclocal.m4
View file @ 881bc15b
# generated automatically by aclocal 1.14 -*- Autoconf -*-
# generated automatically by aclocal 1.16.1 -*- Autoconf -*-
# Copyright (C) 1996-2013 Free Software Foundation, Inc.
# Copyright (C) 1996-2018 Free Software Foundation, Inc.
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -20,7 +20,7 @@ You have another version of autoconf. It may work, but is not guaranteed to.
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......@@ -32,10 +32,10 @@ To do so, use the procedure documented by the package, typically 'autoreconf'.])
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[AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
])
......@@ -51,14 +51,14 @@ m4_define([_AM_AUTOCONF_VERSION], [])
# Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
# This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
[AM_AUTOMAKE_VERSION([1.14])dnl
[AM_AUTOMAKE_VERSION([1.16.1])dnl
m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
# AM_AUX_DIR_EXPAND -*- Autoconf -*-
# Copyright (C) 2001-2013 Free Software Foundation, Inc.
# Copyright (C) 2001-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -103,15 +103,14 @@ _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
# configured tree to be moved without reconfiguration.
AC_DEFUN([AM_AUX_DIR_EXPAND],
[dnl Rely on autoconf to set up CDPATH properly.
AC_PREREQ([2.50])dnl
# expand $ac_aux_dir to an absolute path
am_aux_dir=`cd $ac_aux_dir && pwd`
[AC_REQUIRE([AC_CONFIG_AUX_DIR_DEFAULT])dnl
# Expand $ac_aux_dir to an absolute path.
am_aux_dir=`cd "$ac_aux_dir" && pwd`
])
# AM_CONDITIONAL -*- Autoconf -*-
# Copyright (C) 1997-2013 Free Software Foundation, Inc.
# Copyright (C) 1997-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -142,7 +141,7 @@ AC_CONFIG_COMMANDS_PRE(
Usually this means the macro was only invoked conditionally.]])
fi])])
# Copyright (C) 1999-2013 Free Software Foundation, Inc.
# Copyright (C) 1999-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -333,13 +332,12 @@ _AM_SUBST_NOTMAKE([am__nodep])dnl
# Generate code to set up dependency tracking. -*- Autoconf -*-
# Copyright (C) 1999-2013 Free Software Foundation, Inc.
# Copyright (C) 1999-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
# _AM_OUTPUT_DEPENDENCY_COMMANDS
# ------------------------------
AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
......@@ -347,49 +345,41 @@ AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
# Older Autoconf quotes --file arguments for eval, but not when files
# are listed without --file. Let's play safe and only enable the eval
# if we detect the quoting.
case $CONFIG_FILES in
*\'*) eval set x "$CONFIG_FILES" ;;
*) set x $CONFIG_FILES ;;
esac
# TODO: see whether this extra hack can be removed once we start
# requiring Autoconf 2.70 or later.
AS_CASE([$CONFIG_FILES],
[*\'*], [eval set x "$CONFIG_FILES"],
[*], [set x $CONFIG_FILES])
shift
for mf
# Used to flag and report bootstrapping failures.
am_rc=0
for am_mf
do
# Strip MF so we end up with the name of the file.
mf=`echo "$mf" | sed -e 's/:.*$//'`
# Check whether this is an Automake generated Makefile or not.
# We used to match only the files named 'Makefile.in', but
# some people rename them; so instead we look at the file content.
# Grep'ing the first line is not enough: some people post-process
# each Makefile.in and add a new line on top of each file to say so.
# Grep'ing the whole file is not good either: AIX grep has a line
am_mf=`AS_ECHO(["$am_mf"]) | sed -e 's/:.*$//'`
# Check whether this is an Automake generated Makefile which includes
# dependency-tracking related rules and includes.
# Grep'ing the whole file directly is not great: AIX grep has a line
# limit of 2048, but all sed's we know have understand at least 4000.
if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
dirpart=`AS_DIRNAME("$mf")`
else
continue
fi
# Extract the definition of DEPDIR, am__include, and am__quote
# from the Makefile without running 'make'.
DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
test -z "$DEPDIR" && continue
am__include=`sed -n 's/^am__include = //p' < "$mf"`
test -z "$am__include" && continue
am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
# Find all dependency output files, they are included files with
# $(DEPDIR) in their names. We invoke sed twice because it is the
# simplest approach to changing $(DEPDIR) to its actual value in the
# expansion.
for file in `sed -n "
s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g'`; do
# Make sure the directory exists.
test -f "$dirpart/$file" && continue
fdir=`AS_DIRNAME(["$file"])`
AS_MKDIR_P([$dirpart/$fdir])
# echo "creating $dirpart/$file"
echo '# dummy' > "$dirpart/$file"
done
sed -n 's,^am--depfiles:.*,X,p' "$am_mf" | grep X >/dev/null 2>&1 \
|| continue
am_dirpart=`AS_DIRNAME(["$am_mf"])`
am_filepart=`AS_BASENAME(["$am_mf"])`
AM_RUN_LOG([cd "$am_dirpart" \
&& sed -e '/# am--include-marker/d' "$am_filepart" \
| $MAKE -f - am--depfiles]) || am_rc=$?
done
if test $am_rc -ne 0; then
AC_MSG_FAILURE([Something went wrong bootstrapping makefile fragments
for automatic dependency tracking. Try re-running configure with the
'--disable-dependency-tracking' option to at least be able to build
the package (albeit without support for automatic dependency tracking).])
fi
AS_UNSET([am_dirpart])
AS_UNSET([am_filepart])
AS_UNSET([am_mf])
AS_UNSET([am_rc])
rm -f conftest-deps.mk
}
])# _AM_OUTPUT_DEPENDENCY_COMMANDS
......@@ -398,18 +388,17 @@ AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
# -----------------------------
# This macro should only be invoked once -- use via AC_REQUIRE.
#
# This code is only required when automatic dependency tracking
# is enabled. FIXME. This creates each '.P' file that we will
# need in order to bootstrap the dependency handling code.
# This code is only required when automatic dependency tracking is enabled.
# This creates each '.Po' and '.Plo' makefile fragment that we'll need in
# order to bootstrap the dependency handling code.
AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
[AC_CONFIG_COMMANDS([depfiles],
[test x"$AMDEP_TRUE" != x"" || _AM_OUTPUT_DEPENDENCY_COMMANDS],
[AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"])
])
[AMDEP_TRUE="$AMDEP_TRUE" MAKE="${MAKE-make}"])])
# Do all the work for Automake. -*- Autoconf -*-
# Copyright (C) 1996-2013 Free Software Foundation, Inc.
# Copyright (C) 1996-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -496,11 +485,11 @@ AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl
AC_REQUIRE([AC_PROG_MKDIR_P])dnl
# For better backward compatibility. To be removed once Automake 1.9.x
# dies out for good. For more background, see:
# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
# <https://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
# <https://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
# We need awk for the "check" target. The system "awk" is bad on
# some platforms.
# We need awk for the "check" target (and possibly the TAP driver). The
# system "awk" is bad on some platforms.
AC_REQUIRE([AC_PROG_AWK])dnl
AC_REQUIRE([AC_PROG_MAKE_SET])dnl
AC_REQUIRE([AM_SET_LEADING_DOT])dnl
......@@ -564,7 +553,7 @@ END
Aborting the configuration process, to ensure you take notice of the issue.
You can download and install GNU coreutils to get an 'rm' implementation
that behaves properly: <http://www.gnu.org/software/coreutils/>.
that behaves properly: <https://www.gnu.org/software/coreutils/>.
If you want to complete the configuration process using your problematic
'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
......@@ -573,7 +562,11 @@ to "yes", and re-run configure.
END
AC_MSG_ERROR([Your 'rm' program is bad, sorry.])
fi
fi])
fi
dnl The trailing newline in this macro's definition is deliberate, for
dnl backward compatibility and to allow trailing 'dnl'-style comments
dnl after the AM_INIT_AUTOMAKE invocation. See automake bug#16841.
])
dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
dnl add the conditional right here, as _AC_COMPILER_EXEEXT may be further
......@@ -602,7 +595,7 @@ for _am_header in $config_headers :; do
done
echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
# Copyright (C) 2001-2013 Free Software Foundation, Inc.
# Copyright (C) 2001-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -613,7 +606,7 @@ echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_co
# Define $install_sh.
AC_DEFUN([AM_PROG_INSTALL_SH],
[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
if test x"${install_sh}" != xset; then
if test x"${install_sh+set}" != xset; then
case $am_aux_dir in
*\ * | *\ *)
install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
......@@ -623,7 +616,7 @@ if test x"${install_sh}" != xset; then
fi
AC_SUBST([install_sh])])
# Copyright (C) 2003-2013 Free Software Foundation, Inc.
# Copyright (C) 2003-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -644,7 +637,7 @@ AC_SUBST([am__leading_dot])])
# Check to see how 'make' treats includes. -*- Autoconf -*-
# Copyright (C) 2001-2013 Free Software Foundation, Inc.
# Copyright (C) 2001-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -652,49 +645,42 @@ AC_SUBST([am__leading_dot])])
# AM_MAKE_INCLUDE()
# -----------------
# Check to see how make treats includes.
# Check whether make has an 'include' directive that can support all
# the idioms we need for our automatic dependency tracking code.
AC_DEFUN([AM_MAKE_INCLUDE],
[am_make=${MAKE-make}
cat > confinc << 'END'
[AC_MSG_CHECKING([whether ${MAKE-make} supports the include directive])
cat > confinc.mk << 'END'
am__doit:
@echo this is the am__doit target
@echo this is the am__doit target >confinc.out
.PHONY: am__doit
END
# If we don't find an include directive, just comment out the code.
AC_MSG_CHECKING([for style of include used by $am_make])
am__include="#"
am__quote=
_am_result=none
# First try GNU make style include.
echo "include confinc" > confmf
# Ignore all kinds of additional output from 'make'.
case `$am_make -s -f confmf 2> /dev/null` in #(
*the\ am__doit\ target*)
am__include=include
am__quote=
_am_result=GNU
;;
esac
# Now try BSD make style include.
if test "$am__include" = "#"; then
echo '.include "confinc"' > confmf
case `$am_make -s -f confmf 2> /dev/null` in #(
*the\ am__doit\ target*)
am__include=.include
am__quote="\""
_am_result=BSD
;;
esac
# BSD make does it like this.
echo '.include "confinc.mk" # ignored' > confmf.BSD
# Other make implementations (GNU, Solaris 10, AIX) do it like this.
echo 'include confinc.mk # ignored' > confmf.GNU
_am_result=no
for s in GNU BSD; do
AM_RUN_LOG([${MAKE-make} -f confmf.$s && cat confinc.out])
AS_CASE([$?:`cat confinc.out 2>/dev/null`],
['0:this is the am__doit target'],
[AS_CASE([$s],
[BSD], [am__include='.include' am__quote='"'],
[am__include='include' am__quote=''])])
if test "$am__include" != "#"; then
_am_result="yes ($s style)"
break
fi
AC_SUBST([am__include])
AC_SUBST([am__quote])
AC_MSG_RESULT([$_am_result])
rm -f confinc confmf
])
done
rm -f confinc.* confmf.*
AC_MSG_RESULT([${_am_result}])
AC_SUBST([am__include])])
AC_SUBST([am__quote])])
# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
# Copyright (C) 1997-2013 Free Software Foundation, Inc.
# Copyright (C) 1997-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -733,7 +719,7 @@ fi
# Helper functions for option handling. -*- Autoconf -*-
# Copyright (C) 2001-2013 Free Software Foundation, Inc.
# Copyright (C) 2001-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -762,7 +748,7 @@ AC_DEFUN([_AM_SET_OPTIONS],
AC_DEFUN([_AM_IF_OPTION],
[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
# Copyright (C) 1999-2013 Free Software Foundation, Inc.
# Copyright (C) 1999-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -809,7 +795,7 @@ AC_LANG_POP([C])])
# For backward compatibility.
AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])
# Copyright (C) 2001-2013 Free Software Foundation, Inc.
# Copyright (C) 2001-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -828,7 +814,7 @@ AC_DEFUN([AM_RUN_LOG],
# Check to make sure that the build environment is sane. -*- Autoconf -*-
# Copyright (C) 1996-2013 Free Software Foundation, Inc.
# Copyright (C) 1996-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -909,7 +895,7 @@ AC_CONFIG_COMMANDS_PRE(
rm -f conftest.file
])
# Copyright (C) 2009-2013 Free Software Foundation, Inc.
# Copyright (C) 2009-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -969,7 +955,7 @@ AC_SUBST([AM_BACKSLASH])dnl
_AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
])
# Copyright (C) 2001-2013 Free Software Foundation, Inc.
# Copyright (C) 2001-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -997,7 +983,7 @@ fi
INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
AC_SUBST([INSTALL_STRIP_PROGRAM])])
# Copyright (C) 2006-2013 Free Software Foundation, Inc.
# Copyright (C) 2006-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -1016,7 +1002,7 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
# Check how to create a tarball. -*- Autoconf -*-
# Copyright (C) 2004-2013 Free Software Foundation, Inc.
# Copyright (C) 2004-2018 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......
configure
View file @ 881bc15b
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.69 for cluster 1.53.
# Generated by GNU Autoconf 2.69 for cluster 1.56.
#
#
# 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='1.53'
PACKAGE_STRING='cluster 1.53'
PACKAGE_VERSION='1.56'
PACKAGE_STRING='cluster 1.56'
PACKAGE_BUGREPORT=''
PACKAGE_URL=''
......@@ -641,7 +641,6 @@ am__nodep
AMDEPBACKSLASH
AMDEP_FALSE
AMDEP_TRUE
am__quote
am__include
DEPDIR
OBJEXT
......@@ -715,7 +714,8 @@ PACKAGE_VERSION
PACKAGE_TARNAME
PACKAGE_NAME
PATH_SEPARATOR
SHELL'
SHELL
am__quote'
ac_subst_files=''
ac_user_opts='
enable_option_checking
......@@ -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 1.53 to adapt to many kinds of systems.
\`configure' configures cluster 1.56 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 $ac_init_help in
short | recursive ) echo "Configuration of cluster 1.53:";;
short | recursive ) echo "Configuration of cluster 1.56:";;
esac
cat <<\_ACEOF
......@@ -1440,7 +1440,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
cluster configure 1.53
cluster configure 1.56
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 1.53, which was
It was created by cluster $as_me 1.56, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
......@@ -2208,7 +2208,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
am__api_version='1.14'
am__api_version='1.16'
ac_aux_dir=
for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
......@@ -2409,8 +2409,8 @@ test "$program_suffix" != NONE &&
ac_script='s/[\\$]/&&/g;s/;s,x,x,$//'
program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
# expand $ac_aux_dir to an absolute path
am_aux_dir=`cd $ac_aux_dir && pwd`
# Expand $ac_aux_dir to an absolute path.
am_aux_dir=`cd "$ac_aux_dir" && pwd`
if test x"${MISSING+set}" != xset; then
case $am_aux_dir in
......@@ -2429,7 +2429,7 @@ else
$as_echo "$as_me: WARNING: 'missing' script is too old or missing" >&2;}
fi
if test x"${install_sh}" != xset; then
if test x"${install_sh+set}" != xset; then
case $am_aux_dir in
*\ * | *\ *)
install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
......@@ -2723,7 +2723,7 @@ fi
# Define the identity of the package.
PACKAGE='cluster'
VERSION='1.53'
VERSION='1.56'
cat >>confdefs.h <<_ACEOF
......@@ -2753,12 +2753,12 @@ MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
# For better backward compatibility. To be removed once Automake 1.9.x
# dies out for good. For more background, see:
# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
# <https://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
# <https://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
mkdir_p='$(MKDIR_P)'
# We need awk for the "check" target. The system "awk" is bad on
# some platforms.
# We need awk for the "check" target (and possibly the TAP driver). The
# system "awk" is bad on some platforms.
# Always define AMTAR for backward compatibility. Yes, it's still used
# in the wild :-( We should find a proper way to deprecate it ...
AMTAR='$${TAR-tar}'
......@@ -2805,7 +2805,7 @@ END
Aborting the configuration process, to ensure you take notice of the issue.
You can download and install GNU coreutils to get an 'rm' implementation
that behaves properly: <http://www.gnu.org/software/coreutils/>.
that behaves properly: <https://www.gnu.org/software/coreutils/>.
If you want to complete the configuration process using your problematic
'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
......@@ -2815,6 +2815,7 @@ END
as_fn_error $? "Your 'rm' program is bad, sorry." "$LINENO" 5
fi
fi
ac_config_headers="$ac_config_headers config.h"
......@@ -3670,45 +3671,45 @@ DEPDIR="${am__leading_dot}deps"
ac_config_commands="$ac_config_commands depfiles"
am_make=${MAKE-make}
cat > confinc << 'END'
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} supports the include directive" >&5
$as_echo_n "checking whether ${MAKE-make} supports the include directive... " >&6; }
cat > confinc.mk << 'END'
am__doit:
@echo this is the am__doit target
@echo this is the am__doit target >confinc.out
.PHONY: am__doit
END
# If we don't find an include directive, just comment out the code.
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5
$as_echo_n "checking for style of include used by $am_make... " >&6; }
am__include="#"
am__quote=
_am_result=none
# First try GNU make style include.
echo "include confinc" > confmf
# Ignore all kinds of additional output from 'make'.
case `$am_make -s -f confmf 2> /dev/null` in #(
*the\ am__doit\ target*)
am__include=include
am__quote=
_am_result=GNU
;;
esac
# Now try BSD make style include.
if test "$am__include" = "#"; then
echo '.include "confinc"' > confmf
case `$am_make -s -f confmf 2> /dev/null` in #(
*the\ am__doit\ target*)
am__include=.include
am__quote="\""
_am_result=BSD
# BSD make does it like this.
echo '.include "confinc.mk" # ignored' > confmf.BSD
# Other make implementations (GNU, Solaris 10, AIX) do it like this.
echo 'include confinc.mk # ignored' > confmf.GNU
_am_result=no
for s in GNU BSD; do
{ echo "$as_me:$LINENO: ${MAKE-make} -f confmf.$s && cat confinc.out" >&5
(${MAKE-make} -f confmf.$s && cat confinc.out) >&5 2>&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }
case $?:`cat confinc.out 2>/dev/null` in #(
'0:this is the am__doit target') :
case $s in #(
BSD) :
am__include='.include' am__quote='"' ;; #(
*) :
am__include='include' am__quote='' ;;
esac ;; #(
*) :
;;
esac
if test "$am__include" != "#"; then
_am_result="yes ($s style)"
break
fi
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5
$as_echo "$_am_result" >&6; }
rm -f confinc confmf
done
rm -f confinc.* confmf.*
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: ${_am_result}" >&5
$as_echo "${_am_result}" >&6; }
# Check whether --enable-dependency-tracking was given.
if test "${enable_dependency_tracking+set}" = set; then :
......@@ -6008,7 +6009,7 @@ cat >>$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 1.53, which was
This file was extended by cluster $as_me 1.56, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
......@@ -6074,7 +6075,7 @@ _ACEOF
cat >>$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 1.53
cluster config.status 1.56
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
......@@ -6193,7 +6194,7 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
#
# INIT-COMMANDS
#
AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"
AMDEP_TRUE="$AMDEP_TRUE" MAKE="${MAKE-make}"
_ACEOF
......@@ -6807,29 +6808,35 @@ $as_echo "$as_me: executing $ac_file commands" >&6;}
# Older Autoconf quotes --file arguments for eval, but not when files
# are listed without --file. Let's play safe and only enable the eval
# if we detect the quoting.
case $CONFIG_FILES in
*\'*) eval set x "$CONFIG_FILES" ;;
*) set x $CONFIG_FILES ;;
# TODO: see whether this extra hack can be removed once we start
# requiring Autoconf 2.70 or later.
case $CONFIG_FILES in #(
*\'*) :
eval set x "$CONFIG_FILES" ;; #(
*) :
set x $CONFIG_FILES ;; #(
*) :
;;
esac
shift
for mf
# Used to flag and report bootstrapping failures.
am_rc=0
for am_mf
do
# Strip MF so we end up with the name of the file.
mf=`echo "$mf" | sed -e 's/:.*$//'`
# Check whether this is an Automake generated Makefile or not.
# We used to match only the files named 'Makefile.in', but
# some people rename them; so instead we look at the file content.
# Grep'ing the first line is not enough: some people post-process
# each Makefile.in and add a new line on top of each file to say so.
# Grep'ing the whole file is not good either: AIX grep has a line
am_mf=`$as_echo "$am_mf" | sed -e 's/:.*$//'`
# Check whether this is an Automake generated Makefile which includes
# dependency-tracking related rules and includes.
# Grep'ing the whole file directly is not great: AIX grep has a line
# limit of 2048, but all sed's we know have understand at least 4000.
if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
dirpart=`$as_dirname -- "$mf" ||
$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
X"$mf" : 'X\(//\)[^/]' \| \
X"$mf" : 'X\(//\)$' \| \
X"$mf" : 'X\(/\)' \| . 2>/dev/null ||
$as_echo X"$mf" |
sed -n 's,^am--depfiles:.*,X,p' "$am_mf" | grep X >/dev/null 2>&1 \
|| continue
am_dirpart=`$as_dirname -- "$am_mf" ||
$as_expr X"$am_mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
X"$am_mf" : 'X\(//\)[^/]' \| \
X"$am_mf" : 'X\(//\)$' \| \
X"$am_mf" : 'X\(/\)' \| . 2>/dev/null ||
$as_echo X"$am_mf" |
sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
s//\1/
q
......@@ -6847,53 +6854,48 @@ $as_echo X"$mf" |
q
}
s/.*/./; q'`
else
continue
fi
# Extract the definition of DEPDIR, am__include, and am__quote
# from the Makefile without running 'make'.
DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
test -z "$DEPDIR" && continue
am__include=`sed -n 's/^am__include = //p' < "$mf"`
test -z "$am__include" && continue
am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
# Find all dependency output files, they are included files with
# $(DEPDIR) in their names. We invoke sed twice because it is the
# simplest approach to changing $(DEPDIR) to its actual value in the
# expansion.
for file in `sed -n "
s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g'`; do
# Make sure the directory exists.
test -f "$dirpart/$file" && continue
fdir=`$as_dirname -- "$file" ||
$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
X"$file" : 'X\(//\)[^/]' \| \
X"$file" : 'X\(//\)$' \| \
X"$file" : 'X\(/\)' \| . 2>/dev/null ||
$as_echo X"$file" |
sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
s//\1/
q
}
/^X\(\/\/\)[^/].*/{
am_filepart=`$as_basename -- "$am_mf" ||
$as_expr X/"$am_mf" : '.*/\([^/][^/]*\)/*$' \| \
X"$am_mf" : 'X\(//\)$' \| \
X"$am_mf" : 'X\(/\)' \| . 2>/dev/null ||
$as_echo X/"$am_mf" |
sed '/^.*\/\([^/][^/]*\)\/*$/{
s//\1/
q
}
/^X\(\/\/\)$/{
/^X\/\(\/\/\)$/{
s//\1/
q
}
/^X\(\/\).*/{
/^X\/\(\/\).*/{
s//\1/
q
}
s/.*/./; q'`
as_dir=$dirpart/$fdir; as_fn_mkdir_p
# echo "creating $dirpart/$file"
echo '# dummy' > "$dirpart/$file"
done
{ echo "$as_me:$LINENO: cd "$am_dirpart" \
&& sed -e '/# am--include-marker/d' "$am_filepart" \
| $MAKE -f - am--depfiles" >&5
(cd "$am_dirpart" \
&& sed -e '/# am--include-marker/d' "$am_filepart" \
| $MAKE -f - am--depfiles) >&5 2>&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } || am_rc=$?
done
if test $am_rc -ne 0; then
{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
as_fn_error $? "Something went wrong bootstrapping makefile fragments
for automatic dependency tracking. Try re-running configure with the
'--disable-dependency-tracking' option to at least be able to build
the package (albeit without support for automatic dependency tracking).
See \`config.log' for more details" "$LINENO" 5; }
fi
{ am_dirpart=; unset am_dirpart;}
{ am_filepart=; unset am_filepart;}
{ am_mf=; unset am_mf;}
{ am_rc=; unset am_rc;}
rm -f conftest-deps.mk
}
;;
......
configure.ac
View file @ 881bc15b
# Process this file with autoconf to produce a configure script.
AC_INIT(cluster, 1.53)
AC_INIT(cluster, 1.56)
AC_CONFIG_SRCDIR(src/cluster.c)
AM_INIT_AUTOMAKE
AC_CONFIG_HEADERS(config.h)
......
debian/changelog
View file @ 881bc15b
cluster3 (1.56-1) unstable; urgency=medium
* New upstream version
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Remove unnecessary get-orig-source target
* XS-Autobuild: s/no/yes/
-- Andreas Tille <tille@debian.org> Thu, 27 Sep 2018 10:57:23 +0200
cluster3 (1.53-1) unstable; urgency=medium
* New upstream version
......
debian/control
View file @ 881bc15b
......@@ -5,9 +5,9 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
Thorsten Alteholz <debian@alteholz.de>,
Andreas Tille <tille@debian.org>
Section: non-free/science
XS-Autobuild: no
XS-Autobuild: yes
Priority: optional
Build-Depends: debhelper (>= 10),
Build-Depends: debhelper (>= 11~),
libmotif-dev,
perl,
libx11-dev,
......@@ -18,9 +18,9 @@ Build-Depends: debhelper (>= 10),
python-minimal,
python-setuptools,
python-numpy
Standards-Version: 4.1.0
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/cluster3.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/cluster3.git
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/cluster3
Vcs-Git: https://salsa.debian.org/med-team/cluster3.git
Homepage: http://bonsai.hgc.jp/~mdehoon/software/cluster/
Package: cluster3
......
debian/copyright
View file @ 881bc15b
......@@ -2,6 +2,9 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: cluster
Upstream-Contact: M. J. L. de Hoon <mdehoon@ims.u-tokyo.ac.jp>
Source: http://bonsai.hgc.jp/~mdehoon/software/cluster/
Comment: The GUI part of this program is non-free. This was discussed
on the Debian Med mailing list with upstream
https://lists.debian.org/debian-med/2016/02/msg00000.html
Files: *
Copyright: M. J. L. de Hoon <mdehoon@ims.u-tokyo.ac.jp>, S. Imoto, J. Nolan, and S. Miyano, Michael Eisen
......
debian/rules
View file @ 881bc15b
......@@ -54,7 +54,3 @@ override_dh_install:
find debian/$(DEB_SOURCE)/usr -type d -name cluster | xargs rm -rf
# upstream Makefile installs executable cluster in /usr/bin - conflicting name, we are using cluster3
find debian/$(DEB_SOURCE)/usr/bin -type f -name cluster -delete
get-orig-source:
mkdir -p ../tarballs
uscan --verbose --force-download --destdir=../tarballs
doc/Makefile
View file @ 881bc15b
......@@ -5,11 +5,11 @@ all: cluster3.pdf cluster.pdf
cluster3.pdf: cluster3.texinfo $(patsubst $(imagesrc)/%.png,images/%.eps,$(figures))
tex cluster3.texinfo
dvipdfm cluster3
dvipdf cluster3
cluster.pdf: cluster.texinfo
tex cluster.texinfo
dvipdfm cluster
dvipdf cluster
$(patsubst $(imagesrc)/%.png,images/%.eps,$(figures)): images/%.eps: $(imagesrc)/%.png
mkdir -p images
......
doc/cluster.pdf
View file @ 881bc15b
No preview for this file type