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complearn 0.6.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (104) hide show

data/AUTHORS +13 -0
data/COPYING +340 -0
data/ChangeLog +0 -0
data/INSTALL +231 -0
data/Makefile +352 -0
data/Makefile.am +76 -0
data/Makefile.in +352 -0
data/NEWS +7 -0
data/README +0 -0
data/aclocal.m4 +104 -0
data/bin/Makefile +209 -0
data/bin/Makefile.am +8 -0
data/bin/Makefile.in +209 -0
data/bin/labeltree +68 -0
data/bin/labeltree.in +68 -0
data/bin/makesvm +70 -0
data/bin/makesvm.in +70 -0
data/bin/maketree +98 -0
data/bin/maketree.in +98 -0
data/bin/ncd +43 -0
data/bin/ncd.in +43 -0
data/bin/ncdmatrix +54 -0
data/bin/ncdmatrix.in +54 -0
data/bin/ncdvector +50 -0
data/bin/ncdvector.in +50 -0
data/complearn-0.6.2.gem +0 -0
data/complearn.gemspec +57 -0
data/config.log +597 -0
data/config.status +1082 -0
data/configure +4922 -0
data/configure.ac +91 -0
data/confstat5FpLBf/config.h +65 -0
data/confstat5FpLBf/subs-1.sed +50 -0
data/confstat5FpLBf/subs-2.sed +13 -0
data/confstat5FpLBf/subs.frag +0 -0
data/confstat5FpLBf/subs.sed +59 -0
data/confstat5FpLBf/undefs.sed +24 -0
data/doc/FAQ.txt +67 -0
data/doc/Makefile +286 -0
data/doc/Makefile.am +11 -0
data/doc/Makefile.in +286 -0
data/doc/devguide.txt +15 -0
data/doc/example.complearnrc +14 -0
data/doc/examples.txt +35 -0
data/doc/man/Makefile +255 -0
data/doc/man/Makefile.am +11 -0
data/doc/man/Makefile.in +255 -0
data/doc/man/complearn.5 +91 -0
data/doc/man/labeltree.1 +35 -0
data/doc/man/makesvm.1 +60 -0
data/doc/man/maketree.1 +58 -0
data/doc/man/ncd.1 +51 -0
data/doc/man/ncdmatrix.1 +40 -0
data/doc/man/ncdvector.1 +42 -0
data/doc/readme.txt +101 -0
data/doc/userguide.txt +46 -0
data/examples/genes/blueWhale.txt +1 -0
data/examples/genes/cat.txt +1 -0
data/examples/genes/chimpanzee.txt +1 -0
data/examples/genes/finWhale.txt +1 -0
data/examples/genes/graySeal.txt +1 -0
data/examples/genes/harborSeal.txt +1 -0
data/examples/genes/horse.txt +1 -0
data/examples/genes/human.txt +1 -0
data/examples/genes/mouse.txt +1 -0
data/examples/genes/rat.txt +1 -0
data/ext/Makefile +167 -0
data/ext/Quartet.c +399 -0
data/ext/Quartet.h +62 -0
data/ext/TreeScore.c +244 -0
data/ext/TreeScore.h +3 -0
data/ext/config.h +65 -0
data/ext/config.h.in +64 -0
data/ext/extconf.rb +3 -0
data/ext/lib/CompLearnLib/CLConfig.rb +241 -0
data/ext/lib/CompLearnLib/CompressionObject.rb +59 -0
data/ext/lib/CompLearnLib/CompressionTask.rb +99 -0
data/ext/lib/CompLearnLib/DistMatrix.rb +18 -0
data/ext/lib/CompLearnLib/FoundComp.rb +10 -0
data/ext/lib/CompLearnLib/FoundComp.rb.in +10 -0
data/ext/lib/CompLearnLib/Ncd.rb +248 -0
data/ext/lib/CompLearnLib/RunEnv.rb +150 -0
data/ext/lib/CompLearnLib/Task.rb +39 -0
data/ext/lib/CompLearnLib/TaskMaster.rb +13 -0
data/ext/lib/CompLearnLib/TaskMasterMPI.rb +112 -0
data/ext/lib/CompLearnLib/TaskMasterSingle.rb +39 -0
data/ext/lib/CompLearnLib/Tree.rb +300 -0
data/install-sh +294 -0
data/missing +336 -0
data/mkinstalldirs +111 -0
data/o +24 -0
data/scripts/CompLearn.iss +89 -0
data/scripts/CompLearn.iss.in +89 -0
data/scripts/debian/changelog +6 -0
data/scripts/debian/control +14 -0
data/scripts/makeSetup.sh +23 -0
data/scripts/makeSetup.sh.in +23 -0
data/scripts/makedeb.zsh +46 -0
data/scripts/makedeb.zsh.in +46 -0
data/tests/alltests.rb +2 -0
data/tests/bz2test.rb +516 -0
data/tests/sshagent-test.rb +48 -0
data/tests/tests.rb +275 -0
metadata +164 -0

data/NEWS ADDED

@@ -0,0 +1,7 @@
+--Thu Oct 23 20:02:25 CEST 2003
+The system has finally managed to compile on both
+Debian and Red Hat Linux, so at this point I'm making
+the first public packaged release, version 0.54
+Have a Happy Day!

data/README ADDED

File without changes

data/aclocal.m4 ADDED

@@ -0,0 +1,104 @@
+dnl aclocal.m4 generated automatically by aclocal 1.4-p4
+dnl Copyright (C) 1994, 1995-8, 1999 Free Software Foundation, Inc.
+dnl This file is free software; the Free Software Foundation
+dnl gives unlimited permission to copy and/or distribute it,
+dnl with or without modifications, as long as this notice is preserved.
+dnl This program is distributed in the hope that it will be useful,
+dnl but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+dnl even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+dnl PARTICULAR PURPOSE.
+# Do all the work for Automake.  This macro actually does too much --
+# some checks are only needed if your package does certain things.
+# But this isn't really a big deal.
+# serial 1
+dnl Usage:
+dnl AM_INIT_AUTOMAKE(package,version, [no-define])
+AC_DEFUN(AM_INIT_AUTOMAKE,
+[AC_REQUIRE([AC_PROG_INSTALL])
+PACKAGE=[$1]
+AC_SUBST(PACKAGE)
+VERSION=[$2]
+AC_SUBST(VERSION)
+dnl test to see if srcdir already configured
+if test "`cd $srcdir && pwd`" != "`pwd`" && test -f $srcdir/config.status; then
+  AC_MSG_ERROR([source directory already configured; run "make distclean" there first])
+fi
+ifelse([$3],,
+AC_DEFINE_UNQUOTED(PACKAGE, "$PACKAGE", [Name of package])
+AC_DEFINE_UNQUOTED(VERSION, "$VERSION", [Version number of package]))
+AC_REQUIRE([AM_SANITY_CHECK])
+AC_REQUIRE([AC_ARG_PROGRAM])
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+#
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+# symlink; some systems play weird games with the mod time of symlinks
+# (eg FreeBSD returns the mod time of the symlink's containing
+# directory).
+if (
+   set X `ls -Lt $srcdir/configure conftestfile 2> /dev/null`
+   if test "[$]*" = "X"; then
+      # -L didn't work.
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+   fi
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+      && test "[$]*" != "X conftestfile $srcdir/configure"; then
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+      # if, for instance, CONFIG_SHELL is bash and it inherits a
+      # broken ls alias from the environment.  This has actually
+      # happened.  Such a system could not be considered "sane".
+      AC_MSG_ERROR([ls -t appears to fail.  Make sure there is not a broken
+alias in your environment])
+   fi
+   test "[$]2" = conftestfile
+   )
+then
+   # Ok.
+   :
+else
+   AC_MSG_ERROR([newly created file is older than distributed files!
+Check your system clock])
+fi
+rm -f conftest*
+AC_MSG_RESULT(yes)])
+dnl AM_MISSING_PROG(NAME, PROGRAM, DIRECTORY)
+dnl The program must properly implement --version.
+AC_DEFUN(AM_MISSING_PROG,
+[AC_MSG_CHECKING(for working $2)
+# Run test in a subshell; some versions of sh will print an error if
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+# Redirect stdin to placate older versions of autoconf.  Sigh.
+if ($2 --version) < /dev/null > /dev/null 2>&1; then
+   $1=$2
+   AC_MSG_RESULT(found)
+else
+   $1="$3/missing $2"
+   AC_MSG_RESULT(missing)
+fi
+AC_SUBST($1)])

data/bin/Makefile ADDED

@@ -0,0 +1,209 @@
+# Makefile.in generated automatically by automake 1.4-p4 from Makefile.am
+# Copyright (C) 1994, 1995-8, 1999 Free Software Foundation, Inc.
+# This Makefile.in 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.
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+SHELL = /bin/sh
+srcdir = .
+top_srcdir = ..
+prefix = /usr/local
+exec_prefix = ${prefix}
+bindir = ${exec_prefix}/bin
+sbindir = ${exec_prefix}/sbin
+libexecdir = ${exec_prefix}/libexec
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+localstatedir = ${prefix}/var
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+mandir = ${prefix}/man
+includedir = ${prefix}/include
+oldincludedir = /usr/include
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+pkgdatadir = $(datadir)/complearn
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+AUTOHEADER = autoheader
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+INSTALL_PROGRAM = ${INSTALL} $(AM_INSTALL_PROGRAM_FLAGS)
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_SCRIPT = ${INSTALL}
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+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
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+CC = gcc
+FOUNDBZIP2 = true
+FOUNDGZIP = true
+MAKEINFO = makeinfo
+PACKAGE = complearn
+RANLIB = ranlib
+RUBYBIN = /usr/bin/ruby1.8
+SET_MAKE =
+TOPDIR = /home/cilibrar/src/complearngem/complearn-0.6.2
+VERSION = 0.6.2
+WINBUILDDIR = c:\build
+bin_SCRIPTS =  labeltree makesvm maketree ncd ncdmatrix ncdvector
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_CLEAN_FILES =  ncd ncdvector ncdmatrix labeltree maketree makesvm
+SCRIPTS =  $(bin_SCRIPTS)
+DIST_COMMON =  Makefile.am Makefile.in labeltree.in makesvm.in \
+maketree.in ncd.in ncdmatrix.in ncdvector.in
+DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
+TAR = tar
+GZIP_ENV = --best
+all: all-redirect
+.SUFFIXES:
+$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.ac $(ACLOCAL_M4)
+	cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps bin/Makefile
+Makefile: $(srcdir)/Makefile.in  $(top_builddir)/config.status
+	cd $(top_builddir) \
+	  && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+ncd: $(top_builddir)/config.status ncd.in
+	cd $(top_builddir) && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+ncdvector: $(top_builddir)/config.status ncdvector.in
+	cd $(top_builddir) && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+ncdmatrix: $(top_builddir)/config.status ncdmatrix.in
+	cd $(top_builddir) && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+labeltree: $(top_builddir)/config.status labeltree.in
+	cd $(top_builddir) && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+maketree: $(top_builddir)/config.status maketree.in
+	cd $(top_builddir) && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+makesvm: $(top_builddir)/config.status makesvm.in
+	cd $(top_builddir) && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+install-binSCRIPTS: $(bin_SCRIPTS)
+	@$(NORMAL_INSTALL)
+	$(mkinstalldirs) $(DESTDIR)$(bindir)
+	@list='$(bin_SCRIPTS)'; for p in $$list; do \
+	  if test -f $$p; then \
+	    echo " $(INSTALL_SCRIPT) $$p $(DESTDIR)$(bindir)/`echo $$p|sed '$(transform)'`"; \
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+	    $(INSTALL_SCRIPT) $(srcdir)/$$p $(DESTDIR)$(bindir)/`echo $$p|sed '$(transform)'`; \
+	  else :; fi; fi; \
+	done
+uninstall-binSCRIPTS:
+	@$(NORMAL_UNINSTALL)
+	list='$(bin_SCRIPTS)'; for p in $$list; do \
+	  rm -f $(DESTDIR)$(bindir)/`echo $$p|sed '$(transform)'`; \
+	done
+tags: TAGS
+TAGS:
+distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
+subdir = bin
+distdir: $(DISTFILES)
+	@for file in $(DISTFILES); do \
+	  d=$(srcdir); \
+	  if test -d $$d/$$file; then \
+	    cp -pr $$d/$$file $(distdir)/$$file; \
+	  else \
+	    test -f $(distdir)/$$file \
+	    || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
+	    || cp -p $$d/$$file $(distdir)/$$file || :; \
+	  fi; \
+	done
+info-am:
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+install-data-am:
+install-data: install-data-am
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+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+install: install-am
+uninstall-am: uninstall-binSCRIPTS
+uninstall: uninstall-am
+all-am: Makefile $(SCRIPTS)
+all-redirect: all-am
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
+installdirs:
+	$(mkinstalldirs)  $(DESTDIR)$(bindir)
+mostlyclean-generic:
+clean-generic:
+distclean-generic:
+	-rm -f Makefile $(CONFIG_CLEAN_FILES)
+	-rm -f config.cache config.log stamp-h stamp-h[0-9]*
+maintainer-clean-generic:
+mostlyclean-am:  mostlyclean-generic
+mostlyclean: mostlyclean-am
+clean-am:  clean-generic mostlyclean-am
+clean: clean-am
+distclean-am:  distclean-generic clean-am
+distclean: distclean-am
+maintainer-clean-am:  maintainer-clean-generic distclean-am
+	@echo "This command is intended for maintainers to use;"
+	@echo "it deletes files that may require special tools to rebuild."
+maintainer-clean: maintainer-clean-am
+.PHONY: uninstall-binSCRIPTS install-binSCRIPTS tags distdir info-am \
+info dvi-am dvi check check-am installcheck-am installcheck \
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+# 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.
+.NOEXPORT:

data/bin/Makefile.am ADDED

@@ -0,0 +1,8 @@
+bin_SCRIPTS = \
+labeltree \
+makesvm \
+maketree \
+ncd \
+ncdmatrix \
+ncdvector

data/bin/Makefile.in ADDED

@@ -0,0 +1,209 @@
+# Makefile.in generated automatically by automake 1.4-p4 from Makefile.am
+# Copyright (C) 1994, 1995-8, 1999 Free Software Foundation, Inc.
+# This Makefile.in 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.
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+SHELL = @SHELL@
+srcdir = @srcdir@
+top_srcdir = @top_srcdir@
+VPATH = @srcdir@
+prefix = @prefix@
+exec_prefix = @exec_prefix@
+bindir = @bindir@
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+libexecdir = @libexecdir@
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+includedir = @includedir@
+oldincludedir = /usr/include
+DESTDIR =
+pkgdatadir = $(datadir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+top_builddir = ..
+ACLOCAL = @ACLOCAL@
+AUTOCONF = @AUTOCONF@
+AUTOMAKE = @AUTOMAKE@
+AUTOHEADER = @AUTOHEADER@
+INSTALL = @INSTALL@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+transform = @program_transform_name@
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
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+CC = @CC@
+FOUNDBZIP2 = @FOUNDBZIP2@
+FOUNDGZIP = @FOUNDGZIP@
+MAKEINFO = @MAKEINFO@
+PACKAGE = @PACKAGE@
+RANLIB = @RANLIB@
+RUBYBIN = @RUBYBIN@
+SET_MAKE = @SET_MAKE@
+TOPDIR = @TOPDIR@
+VERSION = @VERSION@
+WINBUILDDIR = @WINBUILDDIR@
+bin_SCRIPTS =  labeltree makesvm maketree ncd ncdmatrix ncdvector
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_CLEAN_FILES =  ncd ncdvector ncdmatrix labeltree maketree makesvm
+SCRIPTS =  $(bin_SCRIPTS)
+DIST_COMMON =  Makefile.am Makefile.in labeltree.in makesvm.in \
+maketree.in ncd.in ncdmatrix.in ncdvector.in
+DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
+TAR = tar
+GZIP_ENV = --best
+all: all-redirect
+.SUFFIXES:
+$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.ac $(ACLOCAL_M4)
+	cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps bin/Makefile
+Makefile: $(srcdir)/Makefile.in  $(top_builddir)/config.status
+	cd $(top_builddir) \
+	  && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+ncd: $(top_builddir)/config.status ncd.in
+	cd $(top_builddir) && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+ncdvector: $(top_builddir)/config.status ncdvector.in
+	cd $(top_builddir) && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+ncdmatrix: $(top_builddir)/config.status ncdmatrix.in
+	cd $(top_builddir) && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+labeltree: $(top_builddir)/config.status labeltree.in
+	cd $(top_builddir) && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+maketree: $(top_builddir)/config.status maketree.in
+	cd $(top_builddir) && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+makesvm: $(top_builddir)/config.status makesvm.in
+	cd $(top_builddir) && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+install-binSCRIPTS: $(bin_SCRIPTS)
+	@$(NORMAL_INSTALL)
+	$(mkinstalldirs) $(DESTDIR)$(bindir)
+	@list='$(bin_SCRIPTS)'; for p in $$list; do \
+	  if test -f $$p; then \
+	    echo " $(INSTALL_SCRIPT) $$p $(DESTDIR)$(bindir)/`echo $$p|sed '$(transform)'`"; \
+	    $(INSTALL_SCRIPT) $$p $(DESTDIR)$(bindir)/`echo $$p|sed '$(transform)'`; \
+	  else if test -f $(srcdir)/$$p; then \
+	    echo " $(INSTALL_SCRIPT) $(srcdir)/$$p $(DESTDIR)$(bindir)/`echo $$p|sed '$(transform)'`"; \
+	    $(INSTALL_SCRIPT) $(srcdir)/$$p $(DESTDIR)$(bindir)/`echo $$p|sed '$(transform)'`; \
+	  else :; fi; fi; \
+	done
+uninstall-binSCRIPTS:
+	@$(NORMAL_UNINSTALL)
+	list='$(bin_SCRIPTS)'; for p in $$list; do \
+	  rm -f $(DESTDIR)$(bindir)/`echo $$p|sed '$(transform)'`; \
+	done
+tags: TAGS
+TAGS:
+distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
+subdir = bin
+distdir: $(DISTFILES)
+	@for file in $(DISTFILES); do \
+	  d=$(srcdir); \
+	  if test -d $$d/$$file; then \
+	    cp -pr $$d/$$file $(distdir)/$$file; \
+	  else \
+	    test -f $(distdir)/$$file \
+	    || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
+	    || cp -p $$d/$$file $(distdir)/$$file || :; \
+	  fi; \
+	done
+info-am:
+info: info-am
+dvi-am:
+dvi: dvi-am
+check-am: all-am
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+	$(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
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+	$(mkinstalldirs)  $(DESTDIR)$(bindir)
+mostlyclean-generic:
+clean-generic:
+distclean-generic:
+	-rm -f Makefile $(CONFIG_CLEAN_FILES)
+	-rm -f config.cache config.log stamp-h stamp-h[0-9]*
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+mostlyclean: mostlyclean-am
+clean-am:  clean-generic mostlyclean-am
+clean: clean-am
+distclean-am:  distclean-generic clean-am
+distclean: distclean-am
+maintainer-clean-am:  maintainer-clean-generic distclean-am
+	@echo "This command is intended for maintainers to use;"
+	@echo "it deletes files that may require special tools to rebuild."
+maintainer-clean: maintainer-clean-am
+.PHONY: uninstall-binSCRIPTS install-binSCRIPTS tags distdir info-am \
+info dvi-am dvi check check-am installcheck-am installcheck \
+install-exec-am install-exec install-data-am install-data install-am \
+install uninstall-am uninstall all-redirect all-am all installdirs \
+mostlyclean-generic distclean-generic clean-generic \
+maintainer-clean-generic clean mostlyclean distclean maintainer-clean
+# 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.
+.NOEXPORT: