RubyGems - complearn - Versions diffs - 0.6.2 - Mend

complearn 0.6.2

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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/AUTHORS ADDED

@@ -0,0 +1,13 @@
+CompLearnLib
+A toolkit for compression-based learning by Rudi Cilibrasi
+Contact [email protected] for more information.
+Please see the doc/ directory for more info, and enjoy!
+Thanks also to:
+julio b. ([email protected]) for Website Design
+Stephanie Wehner ([email protected]) for programming and CVS help

data/COPYING ADDED

@@ -0,0 +1,340 @@
+		    GNU GENERAL PUBLIC LICENSE
+		       Version 2, June 1991
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+     59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+ Everyone is permitted to copy and distribute verbatim copies
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+			    Preamble
+  The licenses for most software are designed to take away your
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+Public License instead of this License.

data/ChangeLog ADDED

File without changes

data/INSTALL ADDED

@@ -0,0 +1,231 @@
+Please see the doc/ directory for more specific installation instructions.
+Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002 Free Software
+Foundation, Inc.
+   This file is free documentation; the Free Software Foundation gives
+unlimited permission to copy, distribute and modify it.
+Basic Installation
+==================
+   These are generic installation instructions.
+   The `configure' shell script attempts to guess correct values for
+various system-dependent variables used during compilation.  It uses
+those values to create a `Makefile' in each directory of the package.
+It may also create one or more `.h' files containing system-dependent
+definitions.  Finally, it creates a shell script `config.status' that
+you can run in the future to recreate the current configuration, and a
+file `config.log' containing compiler output (useful mainly for
+debugging `configure').
+   It can also use an optional file (typically called `config.cache'
+and enabled with `--cache-file=config.cache' or simply `-C') that saves
+the results of its tests to speed up reconfiguring.  (Caching is
+disabled by default to prevent problems with accidental use of stale
+cache files.)
+   If you need to do unusual things to compile the package, please try
+to figure out how `configure' could check whether to do them, and mail
+diffs or instructions to the address given in the `README' so they can
+be considered for the next release.  If you are using the cache, and at
+some point `config.cache' contains results you don't want to keep, you
+may remove or edit it.
+   The file `configure.ac' (or `configure.in') is used to create
+`configure' by a program called `autoconf'.  You only need
+`configure.ac' if you want to change it or regenerate `configure' using
+a newer version of `autoconf'.
+The simplest way to compile this package is:
+  1. `cd' to the directory containing the package's source code and type
+     `./configure' to configure the package for your system.  If you're
+     using `csh' on an old version of System V, you might need to type
+     `sh ./configure' instead to prevent `csh' from trying to execute
+     `configure' itself.
+     Running `configure' takes awhile.  While running, it prints some
+     messages telling which features it is checking for.
+  2. Type `make' to compile the package.
+  3. Optionally, type `make check' to run any self-tests that come with
+     the package.
+  4. Type `make install' to install the programs and any data files and
+     documentation.
+  5. You can remove the program binaries and object files from the
+     source code directory by typing `make clean'.  To also remove the
+     files that `configure' created (so you can compile the package for
+     a different kind of computer), type `make distclean'.  There is
+     also a `make maintainer-clean' target, but that is intended mainly
+     for the package's developers.  If you use it, you may have to get
+     all sorts of other programs in order to regenerate files that came
+     with the distribution.
+Compilers and Options
+=====================
+   Some systems require unusual options for compilation or linking that
+the `configure' script does not know about.  Run `./configure --help'
+for details on some of the pertinent environment variables.
+   You can give `configure' initial values for configuration parameters
+by setting variables in the command line or in the environment.  Here
+is an example:
+     ./configure CC=c89 CFLAGS=-O2 LIBS=-lposix
+   *Note Defining Variables::, for more details.
+Compiling For Multiple Architectures
+====================================
+   You can compile the package for more than one kind of computer at the
+same time, by placing the object files for each architecture in their
+own directory.  To do this, you must use a version of `make' that
+supports the `VPATH' variable, such as GNU `make'.  `cd' to the
+directory where you want the object files and executables to go and run
+the `configure' script.  `configure' automatically checks for the
+source code in the directory that `configure' is in and in `..'.
+   If you have to use a `make' that does not support the `VPATH'
+variable, you have to compile the package for one architecture at a
+time in the source code directory.  After you have installed the
+package for one architecture, use `make distclean' before reconfiguring
+for another architecture.
+Installation Names
+==================
+   By default, `make install' will install the package's files in
+`/usr/local/bin', `/usr/local/man', etc.  You can specify an
+installation prefix other than `/usr/local' by giving `configure' the
+option `--prefix=PATH'.
+   You can specify separate installation prefixes for
+architecture-specific files and architecture-independent files.  If you
+give `configure' the option `--exec-prefix=PATH', the package will use
+PATH as the prefix for installing programs and libraries.
+Documentation and other data files will still use the regular prefix.
+   In addition, if you use an unusual directory layout you can give
+options like `--bindir=PATH' to specify different values for particular
+kinds of files.  Run `configure --help' for a list of the directories
+you can set and what kinds of files go in them.
+   If the package supports it, you can cause programs to be installed
+with an extra prefix or suffix on their names by giving `configure' the
+option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
+Optional Features
+=================
+   Some packages pay attention to `--enable-FEATURE' options to
+`configure', where FEATURE indicates an optional part of the package.
+They may also pay attention to `--with-PACKAGE' options, where PACKAGE
+is something like `gnu-as' or `x' (for the X Window System).  The
+`README' should mention any `--enable-' and `--with-' options that the
+package recognizes.
+   For packages that use the X Window System, `configure' can usually
+find the X include and library files automatically, but if it doesn't,
+you can use the `configure' options `--x-includes=DIR' and
+`--x-libraries=DIR' to specify their locations.
+Specifying the System Type
+==========================
+   There may be some features `configure' cannot figure out
+automatically, but needs to determine by the type of machine the package
+will run on.  Usually, assuming the package is built to be run on the
+_same_ architectures, `configure' can figure that out, but if it prints
+a message saying it cannot guess the machine type, give it the
+`--build=TYPE' option.  TYPE can either be a short name for the system
+type, such as `sun4', or a canonical name which has the form:
+     CPU-COMPANY-SYSTEM
+where SYSTEM can have one of these forms:
+     OS KERNEL-OS
+   See the file `config.sub' for the possible values of each field.  If
+`config.sub' isn't included in this package, then this package doesn't
+need to know the machine type.
+   If you are _building_ compiler tools for cross-compiling, you should
+use the `--target=TYPE' option to select the type of system they will
+produce code for.
+   If you want to _use_ a cross compiler, that generates code for a
+platform different from the build platform, you should specify the
+"host" platform (i.e., that on which the generated programs will
+eventually be run) with `--host=TYPE'.
+Sharing Defaults
+================
+   If you want to set default values for `configure' scripts to share,
+you can create a site shell script called `config.site' that gives
+default values for variables like `CC', `cache_file', and `prefix'.
+`configure' looks for `PREFIX/share/config.site' if it exists, then
+`PREFIX/etc/config.site' if it exists.  Or, you can set the
+`CONFIG_SITE' environment variable to the location of the site script.
+A warning: not all `configure' scripts look for a site script.
+Defining Variables
+==================
+   Variables not defined in a site shell script can be set in the
+environment passed to `configure'.  However, some packages may run
+configure again during the build, and the customized values of these
+variables may be lost.  In order to avoid this problem, you should set
+them in the `configure' command line, using `VAR=value'.  For example:
+     ./configure CC=/usr/local2/bin/gcc
+will cause the specified gcc to be used as the C compiler (unless it is
+overridden in the site shell script).
+`configure' Invocation
+======================
+   `configure' recognizes the following options to control how it
+operates.
+`--help'
+`-h'
+     Print a summary of the options to `configure', and exit.
+`--version'
+`-V'
+     Print the version of Autoconf used to generate the `configure'
+     script, and exit.
+`--cache-file=FILE'
+     Enable the cache: use and save the results of the tests in FILE,
+     traditionally `config.cache'.  FILE defaults to `/dev/null' to
+     disable caching.
+`--config-cache'
+`-C'
+     Alias for `--cache-file=config.cache'.
+`--quiet'
+`--silent'
+`-q'
+     Do not print messages saying which checks are being made.  To
+     suppress all normal output, redirect it to `/dev/null' (any error
+     messages will still be shown).
+`--srcdir=DIR'
+     Look for the package's source code in directory DIR.  Usually
+     `configure' can determine that directory automatically.
+`configure' also accepts some other, not widely useful, options.  Run
+`configure --help' for more details.