RubyGems - complearn - Versions diffs - 0.6.2 - Mend

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

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data/doc/FAQ.txt ADDED

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+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
+[email protected]
+Have fun!
+-Rudi

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+pkgdatadir = $(datadir)/complearn
+pkglibdir = $(libdir)/complearn
+pkgincludedir = $(includedir)/complearn
+top_builddir = ..
+ACLOCAL = aclocal
+AUTOCONF = autoconf
+AUTOMAKE = automake
+AUTOHEADER = autoheader
+INSTALL = /usr/bin/install -c
+INSTALL_PROGRAM = ${INSTALL} $(AM_INSTALL_PROGRAM_FLAGS)
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_SCRIPT = ${INSTALL}
+transform = s,x,x,
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+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
+SUBDIRS = man
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_CLEAN_FILES =
+DIST_COMMON =  Makefile.am Makefile.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 doc/Makefile
+Makefile: $(srcdir)/Makefile.in  $(top_builddir)/config.status
+	cd $(top_builddir) \
+	  && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+# This directory's subdirectories are mostly independent; you can cd
+# into them and run `make' without going through this Makefile.
+# To change the values of `make' variables: instead of editing Makefiles,
+# (1) if the variable is set in `config.status', edit `config.status'
+#     (which will cause the Makefiles to be regenerated when you run `make');
+# (2) otherwise, pass the desired values on the `make' command line.
+all-recursive install-data-recursive install-exec-recursive \
+installdirs-recursive install-recursive uninstall-recursive  \
+check-recursive installcheck-recursive info-recursive dvi-recursive:
+	@set fnord $(MAKEFLAGS); amf=$$2; \
+	dot_seen=no; \
+	target=`echo $@ | sed s/-recursive//`; \
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  echo "Making $$target in $$subdir"; \
+	  if test "$$subdir" = "."; then \
+	    dot_seen=yes; \
+	    local_target="$$target-am"; \
+	  else \
+	    local_target="$$target"; \
+	  fi; \
+	  (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	   || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
+	done; \
+	if test "$$dot_seen" = "no"; then \
+	  $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
+	fi; test -z "$$fail"
+mostlyclean-recursive clean-recursive distclean-recursive \
+maintainer-clean-recursive:
+	@set fnord $(MAKEFLAGS); amf=$$2; \
+	dot_seen=no; \
+	rev=''; list='$(SUBDIRS)'; for subdir in $$list; do \
+	  rev="$$subdir $$rev"; \
+	  test "$$subdir" = "." && dot_seen=yes; \
+	done; \
+	test "$$dot_seen" = "no" && rev=". $$rev"; \
+	target=`echo $@ | sed s/-recursive//`; \
+	for subdir in $$rev; do \
+	  echo "Making $$target in $$subdir"; \
+	  if test "$$subdir" = "."; then \
+	    local_target="$$target-am"; \
+	  else \
+	    local_target="$$target"; \
+	  fi; \
+	  (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	   || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
+	done && test -z "$$fail"
+tags-recursive:
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
+	done
+tags: TAGS
+ID: $(HEADERS) $(SOURCES) $(LISP)
+	list='$(SOURCES) $(HEADERS)'; \
+	unique=`for i in $$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: