Loading AUTHORS +2 −1 Original line number Diff line number Diff line 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, Loading ChangeLog +33 −0 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. 2018.04.14 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 Loading INSTALL +6 −4 Original line number Diff line number Diff line Loading @@ -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 Loading Loading @@ -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 +4 −7 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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 Loading Makefile.in +43 −31 Original line number Diff line number Diff line # 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, Loading @@ -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 '$(MAKELEVEL)'; then \ false; \ elif test -n '$(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 \ ?) ;; \ Loading Loading @@ -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 Loading Loading @@ -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, Loading @@ -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) Loading Loading @@ -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 \ Loading @@ -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 Loading @@ -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) Loading Loading @@ -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'`; \ Loading Loading @@ -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 Loading @@ -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 $(am__post_remove_distdir) dist-zip: distdir Loading @@ -592,7 +601,7 @@ dist dist-all: distcheck: dist case '$(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*) \ Loading @@ -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 \ Loading Loading @@ -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. Loading Loading
AUTHORS +2 −1 Original line number Diff line number Diff line 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, Loading
ChangeLog +33 −0 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. 2018.04.14 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 Loading
INSTALL +6 −4 Original line number Diff line number Diff line Loading @@ -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 Loading Loading @@ -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 +4 −7 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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 Loading
Makefile.in +43 −31 Original line number Diff line number Diff line # 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, Loading @@ -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; \ 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 \ ?) ;; \ Loading Loading @@ -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 Loading Loading @@ -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, Loading @@ -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) Loading Loading @@ -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 \ Loading @@ -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 Loading @@ -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) Loading Loading @@ -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'`; \ Loading Loading @@ -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 Loading @@ -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 Loading @@ -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*) \ Loading @@ -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 \ Loading Loading @@ -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. 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