debian/0000755000000000000000000000000012262342110007157 5ustar debian/compat0000644000000000000000000000000212241575631010372 0ustar 9 debian/orig-tar.sh0000755000000000000000000000052512231134622011247 0ustar #!/bin/sh # called by uscan with '--upstream-version' tar xjf $3 make -C shogun-$2 DEBIAN=yes package-from-release rm -rf $3 shogun-$2 shogun_$2.orig # move to directory 'tarballs' if [ -r .svn/deb-layout ]; then . .svn/deb-layout mv shogun_$2.orig.tar.gz $origDir echo "moved shogun_$2.orig.tar.gz to $origDir" fi debian/README.Debian0000644000000000000000000000105312241575631011234 0ustar This package was initially debianized by Torsten Werner and is now maintained by Soeren Sonnenburg . The nonfree SVMlight files have been removed from the upstream archive. Users seeking for SVMLight may resort to using the included GPDT-SVM as a drop in replacement. It uses a very similar algorithm but in many practical applications was shown to be a lot faster. User documentation is availabe if the shogun-doc package is installed. Just point your browser to /usr/share/doc/shogun-doc-en/html-en/index.html . debian/shogun-cmdline-static.install0000644000000000000000000000003212241344230014745 0ustar debian/tmp/usr/bin/shogun debian/patches/0000755000000000000000000000000012262342110010606 5ustar debian/README.source0000644000000000000000000000267112231134622011347 0ustar This package uses quilt to manage all modifications to the upstream source. Changes are stored in the source package as diffs in debian/patches and applied during the build. To get the fully patched source after unpacking the source package, cd to the root level of the source package and run: quilt push -a The last patch listed in debian/patches/series will become the current patch. To add a new set of changes, first run quilt push -a, and then run: quilt new where is a descriptive name for the patch, used as the filename in debian/patches. Then, for every file that will be modified by this patch, run: quilt add before editing those files. You must tell quilt with quilt add what files will be part of the patch before making changes or quilt will not work properly. After editing the files, run: quilt refresh to save the results as a patch. Alternately, if you already have an external patch and you just want to add it to the build system, run quilt push -a and then: quilt import -P /path/to/patch quilt push -a (add -p 0 to quilt import if needed). as above is the filename to use in debian/patches. The last quilt push -a will apply the patch to make sure it works properly. To remove an existing patch from the list of patches that will be applied, run: quilt delete You may need to run quilt pop -a to unapply patches first before running this command. debian/control0000644000000000000000000002272112262205500010567 0ustar Source: shogun Section: science Priority: optional Maintainer: Soeren Sonnenburg Build-Depends: libatlas-base-dev [!powerpc !alpha !arm !armel !armhf !sh4] | liblapack-dev, libeigen3-dev, debhelper (>= 9), libreadline-dev | libreadline5-dev, ghostscript, libblas-dev, doxygen-latex, graphviz, libglpk-dev, libnlopt-dev, liblzo2-dev, zlib1g-dev, liblzma-dev, libxml2-dev, libjson0-dev, cmake, libarpack2-dev, libsnappy-dev, libhdf5-dev (>= 1.8.8~) | libhdf5-serial-dev, Standards-Version: 3.9.5 Homepage: http://www.shogun-toolbox.org Vcs-Svn: http://bollin.googlecode.com/svn/shogun/trunk/ Vcs-Browser: http://bollin.googlecode.com/svn/shogun/trunk/ Package: libshogun15 Conflicts: libshogunui6, libshogunui5, libshogunui4, libshogunui3, libshogunui2, libshogunui1, libshogunui0 Architecture: any Section: libs Depends: ${shlibs:Depends}, ${misc:Depends} Description: Large Scale Machine Learning Toolbox SHOGUN - is a new machine learning toolbox with focus on large scale kernel methods and especially on Support Vector Machines (SVM) with focus to bioinformatics. It provides a generic SVM object interfacing to several different SVM implementations. Each of the SVMs can be combined with a variety of the many kernels implemented. It can deal with weighted linear combination of a number of sub-kernels, each of which not necessarily working on the same domain, where an optimal sub-kernel weighting can be learned using Multiple Kernel Learning. Apart from SVM 2-class classification and regression problems, a number of linear methods like Linear Discriminant Analysis (LDA), Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to train hidden markov models are implemented. The input feature-objects can be dense, sparse or strings and of type int/short/double/char and can be converted into different feature types. Chains of preprocessors (e.g. substracting the mean) can be attached to each feature object allowing for on-the-fly pre-processing. . SHOGUN comes in different flavours, a stand-a-lone version and also with interfaces to Matlab(tm), R, Octave, Readline and Python. This is the core library with the machine learning methods and ui helpers all interfaces are based on. Package: libshogun-dev Section: libdevel Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libshogun15 (= ${binary:Version}) Description: Large Scale Machine Learning Toolbox SHOGUN - is a new machine learning toolbox with focus on large scale kernel methods and especially on Support Vector Machines (SVM) with focus to bioinformatics. It provides a generic SVM object interfacing to several different SVM implementations. Each of the SVMs can be combined with a variety of the many kernels implemented. It can deal with weighted linear combination of a number of sub-kernels, each of which not necessarily working on the same domain, where an optimal sub-kernel weighting can be learned using Multiple Kernel Learning. Apart from SVM 2-class classification and regression problems, a number of linear methods like Linear Discriminant Analysis (LDA), Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to train hidden markov models are implemented. The input feature-objects can be dense, sparse or strings and of type int/short/double/char and can be converted into different feature types. Chains of preprocessors (e.g. substracting the mean) can be attached to each feature object allowing for on-the-fly pre-processing. . SHOGUN comes in different flavours, a stand-a-lone version and also with interfaces to Matlab(tm), R, Octave, Readline and Python. This package includes the developer files required to create stand-a-lone executables. Package: shogun-doc-en Conflicts: shogun-doc Replaces: shogun-doc Section: doc Architecture: all Recommends: libshogun-dev Depends: ${misc:Depends} Description: Large Scale Machine Learning Toolbox SHOGUN - is a new machine learning toolbox with focus on large scale kernel methods and especially on Support Vector Machines (SVM) with focus to bioinformatics. It provides a generic SVM object interfacing to several different SVM implementations. Each of the SVMs can be combined with a variety of the many kernels implemented. It can deal with weighted linear combination of a number of sub-kernels, each of which not necessarily working on the same domain, where an optimal sub-kernel weighting can be learned using Multiple Kernel Learning. Apart from SVM 2-class classification and regression problems, a number of linear methods like Linear Discriminant Analysis (LDA), Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to train hidden markov models are implemented. The input feature-objects can be dense, sparse or strings and of type int/short/double/char and can be converted into different feature types. Chains of preprocessors (e.g. substracting the mean) can be attached to each feature object allowing for on-the-fly pre-processing. . SHOGUN comes in different flavours, a stand-a-lone version and also with interfaces to Matlab(tm), R, Octave, Readline and Python. This is the English user and developer documentation. Package: shogun-doc-cn Section: doc Architecture: all Recommends: libshogun-dev Depends: ${misc:Depends} Description: Large Scale Machine Learning Toolbox SHOGUN - is a new machine learning toolbox with focus on large scale kernel methods and especially on Support Vector Machines (SVM) with focus to bioinformatics. It provides a generic SVM object interfacing to several different SVM implementations. Each of the SVMs can be combined with a variety of the many kernels implemented. It can deal with weighted linear combination of a number of sub-kernels, each of which not necessarily working on the same domain, where an optimal sub-kernel weighting can be learned using Multiple Kernel Learning. Apart from SVM 2-class classification and regression problems, a number of linear methods like Linear Discriminant Analysis (LDA), Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to train hidden markov models are implemented. The input feature-objects can be dense, sparse or strings and of type int/short/double/char and can be converted into different feature types. Chains of preprocessors (e.g. substracting the mean) can be attached to each feature object allowing for on-the-fly pre-processing. . SHOGUN comes in different flavours, a stand-a-lone version and also with interfaces to Matlab(tm), R, Octave, Readline and Python. This is the Chinese user and developer documentation. Package: libshogun-dbg Breaks: shogun-dbg Replaces: shogun-dbg Section: debug Priority: extra Architecture: any Depends: ${misc:Depends}, libshogun15 (= ${binary:Version}) Description: Large Scale Machine Learning Toolbox SHOGUN - is a new machine learning toolbox with focus on large scale kernel methods and especially on Support Vector Machines (SVM) with focus to bioinformatics. It provides a generic SVM object interfacing to several different SVM implementations. Each of the SVMs can be combined with a variety of the many kernels implemented. It can deal with weighted linear combination of a number of sub-kernels, each of which not necessarily working on the same domain, where an optimal sub-kernel weighting can be learned using Multiple Kernel Learning. Apart from SVM 2-class classification and regression problems, a number of linear methods like Linear Discriminant Analysis (LDA), Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to train hidden markov models are implemented. The input feature-objects can be dense, sparse or strings and of type int/short/double/char and can be converted into different feature types. Chains of preprocessors (e.g. substracting the mean) can be attached to each feature object allowing for on-the-fly pre-processing. . SHOGUN comes in different flavours, a stand-a-lone version and also with interfaces to Matlab(tm), R, Octave, Readline and Python. This package contains debug symbols for all interfaces. Package: shogun-cmdline-static Conflicts: shogun-cmdline Replaces: shogun-cmdline Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libshogun15 (= ${binary:Version}) Description: Large Scale Machine Learning Toolbox SHOGUN - is a new machine learning toolbox with focus on large scale kernel methods and especially on Support Vector Machines (SVM) with focus to bioinformatics. It provides a generic SVM object interfacing to several different SVM implementations. Each of the SVMs can be combined with a variety of the many kernels implemented. It can deal with weighted linear combination of a number of sub-kernels, each of which not necessarily working on the same domain, where an optimal sub-kernel weighting can be learned using Multiple Kernel Learning. Apart from SVM 2-class classification and regression problems, a number of linear methods like Linear Discriminant Analysis (LDA), Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to train hidden markov models are implemented. The input feature-objects can be dense, sparse or strings and of type int/short/double/char and can be converted into different feature types. Chains of preprocessors (e.g. substracting the mean) can be attached to each feature object allowing for on-the-fly pre-processing. . SHOGUN comes in different flavours, a stand-a-lone version and also with interfaces to Matlab(tm), R, Octave, Readline and Python. This is the Readline package. debian/shogun-cmdline-static.examples0000644000000000000000000000004512231134622015122 0ustar examples/documented/cmdline_static/* debian/shogun.10000644000000000000000000000534612231134622010557 0ustar .\" Hey, EMACS: -*- nroff -*- .\" First parameter, NAME, should be all caps .\" Second parameter, SECTION, should be 1-8, maybe w/ subsection .\" other parameters are allowed: see man(7), man(1) .TH SHOGUN 5 "August 1, 2007" .\" Please adjust this date whenever revising the manpage. .\" .\" Some roff macros, for reference: .\" .nh disable hyphenation .\" .hy enable hyphenation .\" .ad l left justify .\" .ad b justify to both left and right margins .\" .nf disable filling .\" .fi enable filling .\" .br insert line break .\" .sp insert n+1 empty lines .\" for manpage-specific macros, see man(7) .SH NAME shogun \- A Large Scale Machine Learning Toolbox .SH SYNOPSIS .B shogun .RI [ options ] .br .SH DESCRIPTION This manual page briefly documents the readline interface of .B shogun . .PP .\" TeX users may be more comfortable with the \fB\fP and .\" \fI\fP escape sequences to invode bold face and italics, .\" respectively. \fBShogun\fP is a large scale machine learning toolbox with focus on large scale kernel methods and especially on Support Vector Machines (SVM) with focus to bioinformatics. It provides a generic SVM object interfacing to several different SVM implementations. Each of the SVMs can be combined with a variety of the many kernels implemented. It can deal with weighted linear combination of a number of sub-kernels, each of which not necessarily working on the same domain, where an optimal sub-kernel weighting can be learned using Multiple Kernel Learning. Apart from SVM 2-class classification and regression problems, a number of linear methods like Linear Discriminant Analysis (LDA), Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to train hidden markov models are implemented. The input feature-objects can be dense, sparse or strings and of type int/short/double/char and can be converted into different feature types. Chains of preprocessors (e.g. substracting the mean) can be attached to each feature object allowing for on-the-fly pre-processing. .SH OPTIONS A summary of options is included below. .TP .B \-h, \-\-help, /? Show summary of options. .TP .B \-i listen on tcp port 7367 (hex of sg) .TP .B filename execute a script by reading commands from file .TP when no options are given the interactive readline interface will be entered .TP .SH SEE ALSO .BR svm-train (1), .BR svm-predict (1). .BR svm-scale (1). .TP .SH AUTHOR .br shogun was written by Soeren Sonnenburg and Gunnar Raetsch .PP This manual page was written by Soeren Sonnenburg , for the Debian project (but may be used by others). debian/copyright0000644000000000000000000002445612241414127011132 0ustar Files: * Copyright: 1999-2009 Fraunhofer Institute FIRST Copyright: 1999-2011 Max Planck Society Copyright: 2009-2011 Berlin Institute of Technology Copyright: 2011-2013 Soeren Sonnenburg, Fernando J. Iglesias, Heiko Strathmann, Sergey Lisitsyn Copyright: 2012 Chiyuan Zhang Copyright: 2012-2013 Viktor Gal, Engeniy Andreev Copyright: 2013 Shell Hu, Zhengyang Liu License: GPL-3+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . On Debian systems, you can find the GPL license in: `/usr/share/common-licenses/GPL'. Files: debian/* Copyright: 2007-2013 Soeren Sonnenburg, Torsten Werner License: GPL-3+ Files: src/shogun/lib/external/shogun_libsvm.* Copyright: 2000-2008 Chih-Chung Chang and Chih-Jen Lin License: BSD-3-clause Copyright (c) 2000-2008 Chih-Chung Chang and Chih-Jen Lin All rights reserved. . Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . 3. Neither name of copyright holders nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. . Quote from the LibSVM homepage: http://www.csie.ntu.edu.tw/~cjlin/libsvm/faq.html#f204 . The libsvm license ("the modified BSD license") is compatible with many free software licenses such as GPL. Hence, it is very easy to use libsvm in your software. It can also be used in commercial products. Files: ./src/shogun/optimization/liblinear/shogun_liblinear.* Files: ./src/shogun/optimization/liblinear/tron.* Copyright: 2007-2008 Machine Learning Group at National Taiwan University Contributors License: BSD-3-clause Copyright (c) 2007-2008 The LIBLINEAR Project. All rights reserved. . Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . 3. Neither name of copyright holders nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: ./src/shogun/lib/external/gpdt* Files: ./src/shogun/lib/external/gpm.* Copyright: 2004-2008 by T. Serafini, G. Zanghirati, L. Zanni. License: GPL-2+ Permission to copy and modify this software and its documentation for internal research use is granted, provided that this notice is retained thereon and on all copies or modifications. The authors and their respective Universities makes no representations as to the suitability and operability of this software for any purpose. It is provided "as is" without express or implied warranty. Use of this software for commercial purposes is expressly prohibited without contacting the authors. . This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, you can find the GPL-2 license in: /usr/share/common-licenses/GPL-2 Files: ./src/shogun/lib/external/ssl.* Copyright: 2006 Vikas Sindhwani (vikass@cs.uchicago.edu) License: GPL-2+ Files: ./src/shogun/multiclass/GMNPLib.* Files: ./src/shogun/multiclass/GMNPSVM.* Copyright: 1999-2008 Center for Machine Perception, CTU FEL Prague Licence: GPL-3+ Files: ./src/shogun/classifier/svm/OnlineSVMSGD.* Copyright: 2007 Leon Bottou Licence: LGPL-2.1 This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. . On Debian systems, you can find the LGPL-2.1 license in: /usr/share/common-licenses/LGPL-2.1 Files: ./src/shogun/kernel/string/LocalAlignmentStringKernel.* Copyright: 2005 Jean-Philippe Vert, Hiroto Saigo License: GPL-3+ Files: ./src/shogun/kernel/string/OligoStringKernel.* Copyright: 2008 Christian Igel, Tobias Glasmachers License: GPL-3+ Files: ./src/shogun/lib/Hash.* Copryright: 2009 Soeren Sonnenburg Copyright: 1993 Colin Plumb Copyright: Austin Appleby License: GPL-3+ The contained MD5 and Murmor hashing functions were integrated from public sources. Their respective copyrights follow: . MD5 . This code implements the MD5 message-digest algorithm. The algorithm is due to Ron Rivest. This code was written by Colin Plumb in 1993, no copyright is claimed. This code is in the public domain; do with it what you wish. . Equivalent code is available from RSA Data Security, Inc. This code has been tested against that, and is equivalent, except that you don't need to include two pages of legalese with every copy. . To compute the message digest of a chunk of bytes, declare an MD5Context structure, pass it to MD5Init, call MD5Update as needed on buffers full of bytes, and then call MD5Final, which will fill a supplied 16-byte array with the digest. . MurmurHash2 . (C) Austin Appleby, released under the MIT License . Note - This code makes a few assumptions about how your machine behaves - . 1. We can read a 4-byte value from any address without crashing 2. It will not produce the same results on little-endian and big-endian machines. Files: ./src/shogun/transfer/domain_adaptation/DomainAdaptationSVM.* Copyright: 2007-2009 Max-Planck-Society License: GPL-2+ Files: ./src/shogun/classifier/mkl/MKLMulticlass* Copyright: 2009 Fraunhofer Institute FIRST and Max-Planck-Society License: GPL-3+ Files: ./src/shogun/distance/BrayCurtisDistance.* Files: ./src/shogun/distance/CanberraMetric.* Files: ./src/shogun/distance/ChiSquareDistance.* Files: ./src/shogun/distance/CosineDistance.* Files: ./src/shogun/distance/GeodesicMetric.* Files: ./src/shogun/distance/TanimotoDistance.* Copyright: 2008-2009 Fraunhofer Institute FIRST License: GPL-3+ Files: ./src/shogun/lib/Compressor.* Files: ./src/shogun/features/StringFileFeatures.h Files: ./src/shogun/preproc/DecompressString.h Copyright: 2009 Berlin Institute of Technology License: GPL-3+ Files: ./src/shogun/multiclass/LaRank.* Copyright: 2008- Antoine Bordes Copyright: 2002 Leon Bottou, Yann Le Cun, AT&T Corp, NECI. Copyright: 1987-1999 Leon Bottou and Neuristique. Copyright: 1991-2001 AT&T Corp. License: GPL-2+ Files: ./src/shogun/io/HDF5File.* Files: ./src/shogun/features/HashedWDFeaturesTransposed.* Files: ./src/shogun/features/HashedWDFeatures.* Files: ./src/shogun/features/SNPFeatures.* Copyright: 2010 Berlin Institute of Technology License: GPL-3+ Files: ./src/shogun/kernel/MultitaskKernelMaskPairNormalizer.h Copyright: 2010 Max-Planck-Society License: GPL-2+ Files: ./src/shogun/lib/external/libqp* Copyright: 2006-2008 Vojtech Franc, xfrancv@cmp.felk.cvut.cz License: GPL-3+ Files: ./src/shogun/classifier/svm/SGDQN.* Copyright: 2009- Antoine Bordes License: GPL-2.1 Files: ./src/shogun/classifier/vw/* Files: ./src/shogun/loss/* Files: ./src/shogun/lib/v_array.h Files: ./src/shogun/io/IOBuffer.* Copyright: 2009 Yahoo! Inc. License: BSD-3-clause debian/shogun-cmdline-static.manpages0000644000000000000000000000002012231134622015070 0ustar debian/shogun.1 debian/rules0000755000000000000000000000137112241443425010251 0ustar #!/usr/bin/make -f BUILDDIR = $(CURDIR)/debian/build %: dh $@ --buildsystem=cmake --builddirectory=$(BUILDDIR) override_dh_auto_configure: dh_auto_configure -- -DCMAKE_SKIP_RPATH=TRUE -DBUILD_EXAMPLES=OFF -DUSE_SVMLIGHT=OFF -DCmdLineStatic=ON override_dh_install: $(MAKE) -C doc doc $(RM) doc/html*/*.map $(RM) doc/html*/*.md5 $(RM) doc/html*/installdox $(RM) doc/html*/formula.repository mkdir -p $(CURDIR)/debian/shogun-doc-en/usr/share/doc/shogun-doc-en mkdir -p $(CURDIR)/debian/shogun-doc-cn/usr/share/doc/shogun-doc-cn cp -r doc/html $(CURDIR)/debian/shogun-doc-en/usr/share/doc/shogun-doc-en cp -r doc/html_cn $(CURDIR)/debian/shogun-doc-cn/usr/share/doc/shogun-doc-cn dh_install override_dh_strip: dh_strip --dbg-package=libshogun-dbg debian/source/0000755000000000000000000000000012262342110010457 5ustar debian/source/format0000644000000000000000000000001412231134622011670 0ustar 3.0 (quilt) debian/libshogun-dev.install0000644000000000000000000000007712241344230013323 0ustar debian/tmp/usr/include/shogun debian/tmp/usr/lib/libshogun*.so debian/watch0000644000000000000000000000014112231134622010207 0ustar version=3 http://www.shogun-toolbox.org .*/shogun-([\d\.]+).tar.bz2 \ debian debian/orig-tar.sh debian/changelog0000644000000000000000000004757612262342075011066 0ustar shogun (3.1.1-1) unstable; urgency=low * New upstream version -- Soeren Sonnenburg Sun, 05 Jan 2014 09:35:46 +0100 shogun (3.1.0-1) unstable; urgency=low * New upstream version * Bump standards version to 3.9.5 (no changes required). -- Soeren Sonnenburg Sun, 05 Jan 2014 08:34:52 +0100 shogun (3.0.1~git20131115.557741b-2) unstable; urgency=low * Depend on libglpk-dev. * Bump compat version to 9. * Replace shogun-dbg with libshogun-dbg (Closes: #729705). * Fix minor typo in documentation. -- Soeren Sonnenburg Fri, 15 Nov 2013 17:32:52 +0100 shogun (3.0.1~git20131115.557741b-1) unstable; urgency=low * New upstream version (+additional bugfixes from current git) * Rewrite packaging to use debhelper and cmake: Drop all static and modular interfaces from this source package and do these later for each individual interface with separate source packages to keep shogun in debian. -- Soeren Sonnenburg Fri, 15 Nov 2013 14:28:11 +0100 shogun (1.1.0-6) unstable; urgency=low * Fix error occurring on package upgrades (Closes: #682166) -- Soeren Sonnenburg Sat, 30 Jun 2012 22:52:04 +0200 shogun (1.1.0-5) unstable; urgency=low * Disable 'libatlas-base-dev' build dependency for armhf builds. Thanks Hector Oron for the patch. (Closes: #667468) * Add temporary workaround for FTBFS with ld --as-needed. Thanks Leo Iannacone for the patch. (Closes: #657434) * Upload to unstable. (Closes: #669005) -- Soeren Sonnenburg Tue, 24 Jan 2012 20:19:47 +0100 shogun (1.1.0-4) unstable; urgency=low [ Jo Shields ] * debian/rules: + Include workaround for CDBS throwing away vital packaging data required by dh_clideps to resolve dependencies. * debian/control: + Scrap unneeded manual dependencies on libmono-corlib4.0-cil and libshogun11 (Closes: #657096). [ Soeren Sonnenburg ] * Build depend on libhdf5-dev (>= 1.8.8~) | libhdf5-serial-dev instead of just libhdf5-dev. * Temporarily drop octave build dependencies from debian/control. -- Soeren Sonnenburg Tue, 24 Jan 2012 17:05:48 +0100 shogun (1.1.0-3) unstable; urgency=low * Make csharp package depend on libmono-corlib4.0-cil; remove csharp:Depends or csharp:Provides and use cli:Depends in debian/control (Closes: #656757). -- Soeren Sonnenburg Mon, 23 Jan 2012 09:05:31 +0100 shogun (1.1.0-2) unstable; urgency=low * Build depend on libhdf5-dev instead of libhdf5-serial-dev to accommodate hdf5 transition. * Build depend on mono-devel and cli-common-dev instead of mono2.0-devel and use include cli.make in debian rules. (Closes: #656757). * Use dmcs instead of gmcs (Closes: #656756). -- Soeren Sonnenburg Sun, 22 Jan 2012 19:26:12 +0100 shogun (1.1.0-1) unstable; urgency=low * New upstream version with major feature enhancements. - This fixes liblzma5 transition (Closes: #647753) - Require clang to compile package as gcc/g++ require >3GB to compile the package (Closes: #645249). - Remove patches integrated upstream. - Since octave is failing to compile with clang - temporarily disable shogun's octave interface. * Really replace doxygen and texlive-* build dependencies with doxygen-latex (Closes: #616279). -- Soeren Sonnenburg Wed, 14 Dec 2011 10:04:55 +0100 shogun (1.0.0-1) unstable; urgency=low * New upstream version with major feature enhancements. - Add various upstream patches to fix installation - Rename static interface packages to shogun-interface-static - Create new modular interface packages for java, lua, ruby, c# - Install libshogun examples also for libshogun-dev package - Convert package to use dh_python2 (Closes: #632249). - Enable python packaging for multiple python versions. - Update copyright file to match new contributions. - Bump standards version to 3.9.2 (no changes required). * Replace doxygen and texlive-* build dependencies with doxygen-latex (Closes: #616279) * Acknowledging non-maintainer upload fixing FTBS with newer gcc's (How could this ever compile??!) -- Soeren Sonnenburg Tue, 11 Oct 2011 21:04:30 +0200 shogun (0.10.0-2.1) unstable; urgency=low * Non-maintainer upload. * Apply upstream patch to fix FTBFS with new gcc (closes: #625115). Thanks, Sebastian Ramacher! -- Julien Cristau Fri, 24 Jun 2011 20:30:58 +0200 shogun (0.10.0-2) unstable; urgency=low * Upload to unstable. -- Soeren Sonnenburg Mon, 14 Feb 2011 11:10:50 +0100 shogun (0.10.0-1) experimental; urgency=low * New upstream version with major feature enhancements. - Fix build with ld --as-needed thanks Matthias Klose for the patch. (Closes: #606018) - Cherry pick patches from upstream svn-trunk to fix build failure. -- Soeren Sonnenburg Wed, 12 Jan 2011 17:29:40 +0100 shogun (0.9.3-4) unstable; urgency=high * Workaround cdbs problem and hopefully only create doxygen doc once. - This should be a workaround for the FTBS caused by doxygen bugs. - Therefore increasing urgency to high. -- Soeren Sonnenburg Tue, 17 Aug 2010 21:16:30 +0200 shogun (0.9.3-3) unstable; urgency=low * Do not call make doc on arch-dep targets but on indep only avoiding doxygen doc builds more than once. * Convert package to pysupport and call dh_numpy manually upon install (Closes: #590731). -- Soeren Sonnenburg Fri, 30 Jul 2010 21:16:49 +0200 shogun (0.9.3-2) unstable; urgency=low * Bump standards version to 3.9.1.0 (no changes required). * Use different logic to workaround FTBS with newer doxygen versions (Closes: #590422) * Add upstream patches to - tolerate column vectors in hdf5 (hdf5_tolerate_column_vectors.patch) - fix a invalid free in ocas (ocas_free.patch) - add swig 2.0 support (swig2.0.patch) - wrap python files within the python-modular interface (swig_file_support.patch) - to add further safety checks for the linear kernel (linear_kernel_parameters.patch) -- Soeren Sonnenburg Tue, 27 Jul 2010 09:24:22 +0200 shogun (0.9.3-1) unstable; urgency=low * New upstream version with feature enhancements, cleanups and bugfixes. - soname change requires package renames to libshogun8 and libshogunui5. - Drop patches included upstream. -- Soeren Sonnenburg Mon, 31 May 2010 15:43:45 +0200 shogun (0.9.2-1) unstable; urgency=low * New upstream version with feature enhancements, cleanups and bugfixes. - Switch to dpkg-source 3.0 (quilt) format. - Update copyright. - Drop patches included upstream. - Build depend on libhdf5-serial-dev to support hdf5 based i/o. - Apply patch from svn to fix libshogunui static file. -- Soeren Sonnenburg Mon, 05 Apr 2010 15:33:33 +0200 shogun (0.9.1-2) unstable; urgency=low * Add support fro Renesas SH (thanks Nobuhiro Iwamatsu for the patch configure.diff): (Closes: #568825) * Workaround doxygen FTBS (patch doxygen.diff) (Closes: #568612) * Apply upstream patches to limit training time in libsvm and mc svm (patches libsvm_mc_time_limit.diff, libsvm_time_limit.diff) * Apply upstream patch to fix get_kernel_matrix etc for custom kernels (custom_kernel_init.diff) * Apply upstream patch improving error message (hmm_observations.diff) * Apply upstream patch correcting a wrong liblinear sign flip (sign_flip_liblinear.diff) * Bump standards version (no changes required). -- Soeren Sonnenburg Tue, 09 Feb 2010 09:27:18 +0100 shogun (0.9.1-1) unstable; urgency=low * New upstream version with feature enhancements, cleanups and bugfixes. * Drop configure patch to workaround FTBS (included upstream). * Build depend on liblzo2-dev, zlib1g-dev, liblzma-dev to support shoguns compressed files. * Add patch from upstream svn to fix get_w() and set_w() for linear classifiers. * Use publicly available svn url for debian sources (Closes: #556096). * Rename shogun-doc package to shogun-doc-en and build chinese documentation and include it in package shogun-doc-cn. * Update copyright. -- Soeren Sonnenburg Thu, 19 Nov 2009 15:14:36 +0100 shogun (0.9.0-2) unstable; urgency=low * Add glpk to build depends to enable multiple kerel learning. * Include configure patch to workaround FTBS. -- Soeren Sonnenburg Tue, 27 Oct 2009 14:54:10 +0100 shogun (0.9.0-1) unstable; urgency=low * New upstream version with major feature enhancements, cleanups and documentation updates. * Build depend on libreadline-dev | libreadline5-dev. * Build depend on doxygen (>= 1.6.0). * Build depend on swig (>= 1.3.40). * Drop octave3.0 support and compile for octave3.2. * Update copyright. -- Soeren Sonnenburg Fri, 23 Oct 2009 18:40:05 +0200 shogun (0.8.0-2) unstable; urgency=low * Fix override disparity (put libs in section lib). * Fix linitian warning, shogun-dbg now depends on libshogun and libshogunui. * Build depend on libreadline-dev instead of libreadline5-dev. -- Soeren Sonnenburg Sun, 13 Sep 2009 16:01:04 +0200 shogun (0.8.0-1) unstable; urgency=low [ Torsten Werner ] * Remove myself from Uploaders as discussed with Sören [ Soeren Sonnenburg ] * New upstream version with major feature enhancements, cleanups and documentation updates. * Bump standards version (no changes required). * Minor updates to debian/copyright. -- Soeren Sonnenburg Sun, 16 Aug 2009 10:22:23 +0200 shogun (0.7.3-1) unstable; urgency=low * New upstream bugfix version. * Bump standards version (no changes required). * Remove quilt build-dependency. -- Soeren Sonnenburg Sat, 02 May 2009 22:31:09 +0200 shogun (0.7.2-1) unstable; urgency=low * New upstream version with improved python support. * Move shogun-dbg into section debug. -- Soeren Sonnenburg Thu, 09 Apr 2009 20:11:35 +0200 shogun (0.7.1-1) unstable; urgency=low * New upstream version with major feature enhancements and code re-organization. * Re-organize packaging, split shogun into libshogun0, libshogun0-dev, libshogunui0, libshogunui-dev, shogun-{octave,r,python,cmdline,elwms}, shogun-{octave,python}-modular. * Mention license of .relpath.py. * Include patches from svn-trunk to fix installation. * Mention /usr/share/common-licenses/LGPL-2.1 in copyright. -- Soeren Sonnenburg Sun, 22 Mar 2009 18:50:48 +0100 shogun (0.6.7-1) unstable; urgency=low * New upstream version with code cleanups and bugfixes. * Remove R installation patch (now included upstream). * Add patch from svn-trunk to work around a swig bug, causing a compile failure on 64bit archs. -- Soeren Sonnenburg Wed, 26 Nov 2008 08:23:55 +0100 shogun (0.6.6-2) unstable; urgency=low [ Torsten Werner ] * Add a lintian override for shogun-dbg. [ Soeren Sonnenburg ] * Fix R installation script to avoid problem with update.packages. -- Soeren Sonnenburg Thu, 16 Oct 2008 20:27:02 +0200 shogun (0.6.6-1) unstable; urgency=low [ Soeren Sonnenburg ] * New upstream version with several bugfixes and improved documentation. [ Torsten Werner ] * Remove all patches because they have been applied upstream. -- Torsten Werner Sun, 12 Oct 2008 01:19:35 +0200 shogun (0.6.4-3) unstable; urgency=low * Add build dependency on swig 1.3.36 (Closes: #494335). * Update my email address to sonne@debian.org. * Update copyright. * Version dependency on debhelper (>=5). -- Soeren Sonnenburg Tue, 23 Sep 2008 20:03:32 +0200 shogun (0.6.4-2) unstable; urgency=low * Add patch from svn to fix data-loading in cmdline interface (transpose). -- Soeren Sonnenburg Sun, 17 Aug 2008 21:33:18 +0200 shogun (0.6.4-1) unstable; urgency=low * New upstream version with much improved documentation. * Remove patches as they have been applied upstream. * Add patch from svn to fix running octave test-suite. * Add patch from svn to fix build failure w/o lapack/atlas. -- Soeren Sonnenburg Sat, 16 Aug 2008 11:38:21 +0200 shogun (0.6.3-1) unstable; urgency=low * New upstream bugfix version. * Adapt for new directory layout. * Run tests for all interfaces on make install. * Add doc-base file. * Add patch target and bump Standards Version to 3.8.0. * Add fix from trunk to fix return values in R interface. -- Soeren Sonnenburg Wed, 18 Jun 2008 12:04:16 +0200 shogun (0.6.2-1) unstable; urgency=low * New upstream version with much improved static cmdline,r,python,octave interfaces and several bugfixes. -- Soeren Sonnenburg Fri, 16 May 2008 00:17:04 +0200 shogun (0.6.1-2) unstable; urgency=low * Add README.source documenting we are using quilt for additional patches. * Call dh_pycentral on install not build for shogun-python (fixes FTBS on mips and mipsel with debhelper 7.0.2). -- Soeren Sonnenburg Tue, 29 Apr 2008 08:57:18 +0200 shogun (0.6.1-1) unstable; urgency=low * New upstream version with new octave-modular interface and python-modular speedups * Build depend on swig >= 1.3.35-3 as it contains octave fixes. * Add examples for octave-modular. * Add ghostscript to build-depends which is used to generate .png's from the generated .ps formulas. * Use correct DESTDIR when running tests. * Disable atlas also for arm and armel and fall back to lapack and blas. -- Soeren Sonnenburg Sun, 20 Apr 2008 14:25:25 +0200 shogun (0.6.0-2) unstable; urgency=low [ Torsten Werner ] * Fix output of debian/orig-tar.sh. [ Soeren Sonnenburg ] * Run the python tests after make install. * Include texlive-latex-base to build depends as doxygen requires it to generate images from latex formulas (and does not pull latex in either). * Disable atlas for powerpc and alpha as they FTBFS on these archs. -- Soeren Sonnenburg Tue, 15 Apr 2008 10:12:08 +0200 shogun (0.6.0-1) unstable; urgency=low * New upstream version with major feature enhancements, providing same functionality for all static interfaces and improved user documentation * Pull in atlas dependency whenever available, otherwise fall back to blas and lapack. * Drop sqrtl patch (included upstream). * Don't compress R, octave or python examples -- Soeren Sonnenburg Sun, 13 Apr 2008 11:38:49 +0200 shogun (0.5.1-2) unstable; urgency=high [ Soeren Sonnenburg ] * Add patch from trunk to fix FTBS on mips,mipsel,etc caused by sqrtl not being available for these archs * Add quilt to Build-Depends again * Temporarily remove atlas from Build-Depends for powerpc and alpha and add liblapack-dev to the Build-Depends for these archs [ Torsten Werner ] * Increase urgency because we are fixing FTBFS bugs only. -- Torsten Werner Thu, 20 Mar 2008 13:00:53 +0100 shogun (0.5.1-1) unstable; urgency=low [ Soeren Sonnenburg ] * New upstream version * Get watch file to work * Update build depends for gfortran transition (Closes: #466335) [ Torsten Werner ] * Remove Build-Depends: quilt. -- Torsten Werner Sat, 23 Feb 2008 21:17:20 +0100 shogun (0.5.0-1) unstable; urgency=low * New upstream version with major feature enhancements. * Add !armel ann ameb to atlas3-base-dev build depends (Closes: #460096) * Remove python-numpy-{ext,dev} from build depends and use python-numpy instead (Closes: #463211) * Project switched license to GPLv3, update debian/copyright accordingly * Include missing copyright holders in debian/copyright (Closes: #461616) * Remove depends on xutils-dev as now gcc is used to generate build dependencies * Generate shogun-doc package; add doxygen and graphviz to build depends * Remove patch to fix gcc4.3 compile failure (included upstream) * Enable building of debug package shogun-dbg (Closes: #461614) -- Soeren Sonnenburg Fri, 08 Feb 2008 23:43:33 +0100 shogun (0.4.4-2) unstable; urgency=low [ Soeren Sonnenburg ] * Depend on octave 3.0, thanks Thomas Weber (Closes: #457979) * Fix FTBS for gcc-4.3 (Closes: #458192) [ Torsten Werner ] * Change Depends: liblapack3-dev [arm]. * Support newer versions of dpkg-shlibdeps. * Change XS-Vcs to Vcs in debian/control. -- Torsten Werner Wed, 02 Jan 2008 20:31:20 +0100 shogun (0.4.4-1) unstable; urgency=low * New upstream version contains major bug fixes. -- Soeren Sonnenburg Fri, 23 Nov 2007 13:05:05 +0200 shogun (0.4.3-1) unstable; urgency=low * New upstream allows to disable custom cpu settings which allows for a workaround the gcc-4.2 build failure on alpha. -- Soeren Sonnenburg Fri, 28 Sep 2007 09:53:35 +0200 shogun (0.4.2-1) unstable; urgency=low [Soeren Sonnenburg] * New upstream version (Closes: #442990) * Build R package in a separate directory (Closes: #442730) [Torsten Werner] * minor fixes in debian/rules -- Soeren Sonnenburg Wed, 19 Sep 2007 09:08:42 +0200 shogun (0.4.1-1) unstable; urgency=low * new upstream version -- Soeren Sonnenburg Sat, 01 Sep 2007 09:56:50 +0200 shogun (0.4.0-3) unstable; urgency=low * add manpage for shogun-readline interface -- Soeren Sonnenburg Sun, 05 Aug 2007 13:49:06 +0200 shogun (0.4.0-2) unstable; urgency=low * remove build dependency on octave2.1-forge, but rather make it a Recommends -- Soeren Sonnenburg Thu, 02 Aug 2007 08:25:20 +0200 shogun (0.4.0-1) unstable; urgency=low * new upstream version * also add include matlab examples in the octave examples -- Soeren Sonnenburg Tue, 31 Jul 2007 17:33:47 +0200 shogun (0.3.2-3) unstable; urgency=low * Change Build-Depends: r-base-core from r-base-dev. -- Torsten Werner Sun, 3 Jun 2007 10:50:29 +0200 shogun (0.3.2-2) unstable; urgency=low * support for python 2.5 * bump compat to 5, pycompat to 2 -- Soeren Sonnenburg Wed, 09 May 2007 19:49:26 +0200 shogun (0.3.2-1) unstable; urgency=low * new upstream version -- Torsten Werner Wed, 7 Mar 2007 19:05:03 +0100 shogun (0.3.1-1) unstable; urgency=low * new upstream release, fixes a build problem -- Torsten Werner Tue, 20 Feb 2007 21:01:14 +0100 shogun (0.3.0-1) unstable; urgency=low * new upstream release * Remove Build-Depends: atlas3-base-dev for arm architecture. * Updated debian/python*.examples to reflect upstream changes. -- Torsten Werner Wed, 14 Feb 2007 20:49:23 +0100 shogun (0.2.1+svn1952-1) unstable; urgency=low * new upstream version that builds on more platforms -- Torsten Werner Sun, 11 Feb 2007 16:41:54 +0100 shogun (0.2.1+svn1923-1) unstable; urgency=low * new upstream version * new upstream URL * updated to new build system, renaming the packages to shogun-python-modular and shogun-python -- Soeren Sonnenburg Wed, 24 Jan 2007 10:38:50 +0100 shogun (0.2.1+svn1880-2) unstable; urgency=low * NOT RELEASED YET * Add more python examples. -- Torsten Werner Wed, 10 Jan 2007 22:02:45 +0100 shogun (0.2.1+svn1880-1) unstable; urgency=low [ Torsten Werner ] * new upstream version * Fixed debian/copyright as requested by ftp-master Jörg Jaspert. [ Sören Sonnenburg ] * Removed non-free code completely. * Switch to svn revisions instead of dates. -- Torsten Werner Wed, 10 Jan 2007 20:24:13 +0100 shogun (0.2.1-1) unstable; urgency=low [ Torsten Werner ] * Initial Release, closes: #388148. -- Torsten Werner Thu, 30 Nov 2006 20:20:39 +0100 debian/libshogun15.install0000644000000000000000000000004412262212461012712 0ustar debian/tmp/usr/lib/libshogun*.so.* debian/shogun-doc-en.lintian-overrides0000644000000000000000000000007712231134622015214 0ustar shogun-doc-en: copyright-refers-to-deprecated-bsd-license-file debian/libshogun-dev.examples0000644000000000000000000000004012231134622013462 0ustar examples/documented/libshogun/* debian/shogun-doc.doc-base0000644000000000000000000000251212231134622012627 0ustar Document: shogun Title: Software for Semidefinite Programming Author: Soeren Sonnenburg, Gunnar Raetsch Abstract: SHOGUN - is a new machine learning toolbox with focus on large scale kernel methods and especially on Support Vector Machines (SVM) applied to the field of bioinformatics. It provides a generic SVM object interfacing to several different SVM implementations. Each of the SVMs can be combined with a variety of the many kernels implemented. It can deal with weighted linear combination of a number of sub-kernels, each of which not necessarily working on the same domain, where an optimal sub-kernel weighting can be learned using Multiple Kernel Learning. Apart from SVM 2-class classification and regression problems, a number of linear methods like Linear Discriminant Analysis (LDA), Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to train hidden markov models are implemented. The input feature-objects can be dense, sparse or strings and of type int/short/double/char and can be converted into different feature types. Chains of preprocessors (e.g. substracting the mean) can be attached to each feature object allowing for on-the-fly pre-processing. Section: Science/Data Analysis Format: HTML Index: /usr/share/doc/shogun-doc/html/index.html Files: /usr/share/doc/shogun-doc/html/*.html