complearn 0.6.2

data/configure.ac

@@ -0,0 +1,91 @@
+#                                               -*- Autoconf -*-
+# Process this file with autoconf to produce a configure script.
+
+AC_PREREQ(2.57)
+AC_INIT()
+AC_SUBST(SET_MAKE, MAKE=make)
+TOPDIR=`pwd`
+AC_SUBST(TOPDIR)
+AC_CONFIG_SRCDIR([ext/Quartet.c])
+AM_INIT_AUTOMAKE(complearn,0.6.2)
+AC_CONFIG_HEADERS([ext/config.h])
+
+AC_ARG_ENABLE(winbuild, "Cross compile for windows MinGW/MSYS", winbuild=true, winbuild=false)
+if $winbuild ; then
+	echo "Building for windows"
+else
+	echo "Building for Linux"
+fi
+
+AC_PROG_RANLIB
+
+WINBUILDDIR="c:\build"
+AC_SUBST(WINBUILDDIR)
+
+# Checks for programs.
+AC_PROG_CC
+if $winbuild ; then
+RUBYBIN=/usr/local/bin/ruby
+else
+AC_PATH_PROGS([RUBYBIN], [ruby1.8 ruby])
+fi
+
+AC_MSG_CHECKING([for Ruby bz2 (bzip2) library])
+if $RUBYBIN -e "require 'bz2'" 2>/dev/null; then
+FOUNDBZIP2=true
+else
+FOUNDBZIP2=nil
+fi
+
+echo $FOUNDBZIP2
+AC_SUBST(FOUNDBZIP2)
+
+AC_MSG_CHECKING([for Ruby zlib (gzip) library])
+if $RUBYBIN -e "require 'zlib'" 2>/dev/null ; then
+FOUNDGZIP=true
+else
+FOUNDGZIP=nil
+fi
+echo $FOUNDGZIP
+AC_SUBST(FOUNDGZIP)
+
+if $winbuild ; then
+	FOUNDBZIP=true
+	FOUNDGZIP=true
+fi
+
+# Checks for libraries.
+
+# Checks for header files.
+AC_HEADER_STDC
+AC_CHECK_HEADERS([stdlib.h sys/time.h unistd.h])
+
+# Checks for typedefs, structures, and compiler characteristics.
+AC_HEADER_STDBOOL
+AC_C_CONST
+
+# Checks for library functions.
+
+AC_CONFIG_FILES([Makefile])
+AC_CONFIG_FILES([doc/Makefile])
+AC_CONFIG_FILES([doc/man/Makefile])
+AC_CONFIG_FILES([bin/Makefile])
+AC_CONFIG_FILES([ext/lib/CompLearnLib/FoundComp.rb])
+AC_CONFIG_FILES([bin/ncd],[chmod +x bin/ncd])
+AC_CONFIG_FILES([bin/ncdvector],[chmod +x bin/ncdvector])
+AC_CONFIG_FILES([bin/ncdmatrix],[chmod +x bin/ncdmatrix])
+AC_CONFIG_FILES([bin/labeltree],[chmod +x bin/labeltree])
+AC_CONFIG_FILES([bin/maketree],[chmod +x bin/maketree])
+AC_CONFIG_FILES([bin/makesvm],[chmod +x bin/makesvm])
+AC_CONFIG_FILES([scripts/CompLearn.iss])
+AC_CONFIG_FILES([scripts/makeSetup.sh],[chmod +x scripts/makeSetup.sh])
+AC_CONFIG_FILES([scripts/makedeb.zsh],[chmod +x scripts/makedeb.zsh])
+if $winbuild ; then
+	cp ext/winbuild/Makefile.winbuild ext/Makefile
+else
+AC_CONFIG_COMMANDS([ext/Makefile],[cd $srcdir/ext ; $RUBYBIN extconf.rb ; echo 'distdir:' >> Makefile ], [RUBYBIN=$RUBYBIN])
+fi
+
+#AC_CONFIG_FILES([ext/Makefile])
+
+AC_OUTPUT

data/confstat5FpLBf/config.h

@@ -0,0 +1,65 @@
+/* ext/config.h.  Generated by configure.  */
+/* ext/config.h.in.  Generated from configure.ac by autoheader.  */
+
+/* Define to 1 if you have the <inttypes.h> header file. */
+#define HAVE_INTTYPES_H 1
+
+/* Define to 1 if you have the <memory.h> header file. */
+#define HAVE_MEMORY_H 1
+
+/* Define to 1 if stdbool.h conforms to C99. */
+/* #undef HAVE_STDBOOL_H */
+
+/* Define to 1 if you have the <stdint.h> header file. */
+#define HAVE_STDINT_H 1
+
+/* Define to 1 if you have the <stdlib.h> header file. */
+#define HAVE_STDLIB_H 1
+
+/* Define to 1 if you have the <strings.h> header file. */
+#define HAVE_STRINGS_H 1
+
+/* Define to 1 if you have the <string.h> header file. */
+#define HAVE_STRING_H 1
+
+/* Define to 1 if you have the <sys/stat.h> header file. */
+#define HAVE_SYS_STAT_H 1
+
+/* Define to 1 if you have the <sys/time.h> header file. */
+#define HAVE_SYS_TIME_H 1
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#define HAVE_SYS_TYPES_H 1
+
+/* Define to 1 if you have the <unistd.h> header file. */
+#define HAVE_UNISTD_H 1
+
+/* Define to 1 if the system has the type `_Bool'. */
+/* #undef HAVE__BOOL */
+
+/* Name of package */
+#define PACKAGE "complearn"
+
+/* Define to the address where bug reports for this package should be sent. */
+#define PACKAGE_BUGREPORT ""
+
+/* Define to the full name of this package. */
+#define PACKAGE_NAME ""
+
+/* Define to the full name and version of this package. */
+#define PACKAGE_STRING ""
+
+/* Define to the one symbol short name of this package. */
+#define PACKAGE_TARNAME ""
+
+/* Define to the version of this package. */
+#define PACKAGE_VERSION ""
+
+/* Define to 1 if you have the ANSI C header files. */
+#define STDC_HEADERS 1
+
+/* Version number of package */
+#define VERSION "0.6.2"
+
+/* Define to empty if `const' does not conform to ANSI C. */
+/* #undef const */

data/confstat5FpLBf/subs-1.sed

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data/confstat5FpLBf/subs-2.sed

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data/confstat5FpLBf/subs.sed

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data/confstat5FpLBf/undefs.sed

@@ -0,0 +1,24 @@
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+: clr
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data/doc/FAQ.txt

@@ -0,0 +1,67 @@
+1) Q. The MPI parallel execution environment doesn't seem to be working, why?
+   A. If you are using the bash shell, there is a known problem in that
+bash does not execute ~/.bash_profile in non-interactive shells.  In
+order to fix this, make sure that you set your important environment
+variables (LAMRSH, PATH, LD_LIBRARY_CONFIG, RUBYLIB) inside your ~/.bashrc
+instead.
+
+2) Q. Where can I find out more about the algorithms used in this system?
+   A. Check out our paper: http://www.arxiv.org/abs/cs.SD/0303025
+
+3) Q. What do I need to install in order to run this under Windows?
+   A. First, you must install MinGW, Minimalist GNU for Windows, which can
+      be downloaded from
+        http://www.mingw.org/
+      This version of CompLearn is tested with MinGW-3.1.0-1.exe
+
+      Next, you must install MSYS, the Minimal System for MinGW.
+      The author tests with version MSYS-1.0.10.exe
+
+      It is best to install these two programs in the default locations if
+      possible, as the windows packaging scripts assume default locations for
+      all prerequisite software.
+
+      Finally, you must install Ruby for Windows, MinGW version, from
+        http://ftp.ruby-lang.org/pub/ruby/binaries/mingw/1.8
+      The current version is ruby-1.8.1-20040506-i386-mingw32.tar.gz
+      This is installed from within an MSYS command shell using the command
+        tar xCvfz / ruby-1.8.1-20040506-i386-mingw32.tar.gz
+      Once all these are installed, you may download and install the
+      self-extracting CompLearn windows .exe executable file.
+
+4) Q. What other Debian packages do I need to install to use this software?
+   A. Try:
+apt-get install ruby1.8 zlib1g libbz2-1.0 libiconv-ruby1.8 libyaml-ruby1.8 libbz2-dev libtest-unit-ruby1.8
+dpkg -i libbz2lib-ruby1.8*.deb
+dpkg -i complearn*.deb
+
+5) Q. What sorts of things might this system do well analyzing?
+   A. So far, I have used this system to analyze
+
+a) Musical genres rock/jazz/classical (maketree)
+b) Celtic music classification: jig/reel (makesvm)
+c) Novel author identification (various)
+d) Astronomical data spectral state categorization (various)
+e) Novel translator identification (various)
+f) Written language development (maketree)
+g) Online editorialist authorship identification (makesvm)
+h) Animal kingdom evolutionary trees from genome sequences (maketree)
+i) SARS virus epidemiology (maketree)
+j) Scientific paper subject classification (maketree)
+k) Handwritten digit recognition using NIST special database 19 (makesvm)
+l) File type identification: binary executable, text, bytecode, MIDI
+m) Yeast species-strain / genetic sequence analysis
+n) Network packet categorization, e.g. intrusion detection and monitoring
+
+Clearly, this method can be used in a wide range of applications.
+It is up to you to think of new ways to use it.  If you do find something
+interesting, or have questions, please don't hesitate to let me know by
+email:
+
+Rudi Cilibrasi
+cilibrar@ofb.net
+
+Have fun!
+
+-Rudi
+

data/doc/Makefile

@@ -0,0 +1,286 @@
+# 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
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+
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+DESTDIR =
+
+pkgdatadir = $(datadir)/complearn
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+
+top_builddir = ..
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+
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+	if test "$$dot_seen" = "no"; then \
+	  $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
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+
+mostlyclean-recursive clean-recursive distclean-recursive \
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+	  echo "Making $$target in $$subdir"; \
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+
+tags: TAGS
+
+ID: $(HEADERS) $(SOURCES) $(LISP)
+	list='$(SOURCES) $(HEADERS)'; \
+	unique=`for i in $$list; do echo $$i; done | \
+	  awk '    { files[$$0] = 1; } \
+	       END { for (i in files) print i; }'`; \
+	here=`pwd` && cd $(srcdir) \
+	  && mkid -f$$here/ID $$unique $(LISP)
+
+TAGS: tags-recursive $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) $(LISP)
+	tags=; \
+	here=`pwd`; \
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+   if test "$$subdir" = .; then :; else \
+	    test -f $$subdir/TAGS && tags="$$tags -i $$here/$$subdir/TAGS"; \
+   fi; \
+	done; \
+	list='$(SOURCES) $(HEADERS)'; \
+	unique=`for i in $$list; do echo $$i; done | \
+	  awk '    { files[$$0] = 1; } \
+	       END { for (i in files) print i; }'`; \
+	test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
+	  || (cd $(srcdir) && etags $(ETAGS_ARGS) $$tags  $$unique $(LISP) -o $$here/TAGS)
+
+mostlyclean-tags:
+
+clean-tags:
+
+distclean-tags:
+	-rm -f TAGS ID
+
+maintainer-clean-tags:
+
+distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
+
+subdir = doc
+
+distdir: $(DISTFILES)
+	@for file in $(DISTFILES); do \
+	  d=$(srcdir); \
+	  if test -d $$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)/$$file || :; \
+	  fi; \
+	done
+	for subdir in $(SUBDIRS); do \
+	  if test "$$subdir" = .; then :; else \
+	    test -d $(distdir)/$$subdir \
+	    || mkdir $(distdir)/$$subdir \
+	    || exit 1; \
+	    chmod 777 $(distdir)/$$subdir; \
+	    (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir=../$(top_distdir) distdir=../$(distdir)/$$subdir distdir) \
+	      || exit 1; \
+	  fi; \
+	done
+info-am:
+info: info-recursive
+dvi-am:
+dvi: dvi-recursive
+check-am: all-am
+check: check-recursive
+installcheck-am:
+installcheck: installcheck-recursive
+install-exec-am:
+install-exec: install-exec-recursive
+
+install-data-am:
+install-data: install-data-recursive
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+install: install-recursive
+uninstall-am:
+uninstall: uninstall-recursive
+all-am: Makefile
+all-redirect: all-recursive
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
+installdirs: installdirs-recursive
+installdirs-am:
+
+
+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-tags mostlyclean-generic
+
+mostlyclean: mostlyclean-recursive
+
+clean-am:  clean-tags clean-generic mostlyclean-am
+
+clean: clean-recursive
+
+distclean-am:  distclean-tags distclean-generic clean-am
+
+distclean: distclean-recursive
+
+maintainer-clean-am:  maintainer-clean-tags 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-recursive
+
+.PHONY: install-data-recursive uninstall-data-recursive \
+install-exec-recursive uninstall-exec-recursive installdirs-recursive \
+uninstalldirs-recursive all-recursive check-recursive \
+installcheck-recursive info-recursive dvi-recursive \
+mostlyclean-recursive distclean-recursive clean-recursive \
+maintainer-clean-recursive tags tags-recursive mostlyclean-tags \
+distclean-tags clean-tags maintainer-clean-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-am \
+installdirs mostlyclean-generic distclean-generic clean-generic \
+maintainer-clean-generic clean mostlyclean distclean maintainer-clean
+
+
+rdoc:
+	(cd .. ; rdoc --op doc/rdoc)
+
+www:
+	(cd .. ; rdoc --op www/rdoc)
+
+clean:
+	rm -rf rdoc
+
+# 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: