--- libqsearch-1.0.8.orig/debian/compat +++ libqsearch-1.0.8/debian/compat @@ -0,0 +1 @@ +7 --- libqsearch-1.0.8.orig/debian/control +++ libqsearch-1.0.8/debian/control @@ -0,0 +1,77 @@ +Source: libqsearch +Priority: optional +Maintainer: Debian Science Maintainers +DM-Upload-Allowed: yes +Uploaders: Rudi Cilibrasi , + Andreas Tille +Build-Depends: debhelper (>= 7.1), autotools-dev, libtool, pkg-config, zlib1g-dev, libbz2-dev, + libbz2-1.0, libgsl0-dev, libxml2-dev, libglib2.0-dev, gob2, libcomplearn1, libcomplearn-dev +Standards-Version: 3.8.3 +Section: libs +Vcs-Browser: http://svn.debian.org/wsvn/debian-science/packages/libqsearch/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-science/packages/libqsearch/trunk/ +Homepage: http://complearn.org/ + +Package: libqsearch-gomp-dev +Section: libdevel +Architecture: any +Depends: libqsearch-gomp1 (= ${binary:Version}), libqsearch1-headers (= ${binary:Version}), + libgsl0-dev, pkg-config, libxml2-dev, libglib2.0-dev +Description: CompLearn library, OpenMP version development files + qsearch is a multi-core library for hierarchical clustering. + Using this library, developers can access a tree building system for + genomics, search term clustering, language evolution, music recognition, + and much more + +Package: libqsearch1-headers +Section: libdevel +Architecture: all +Depends: libgsl0-dev, libxml2-dev, libglib2.0-dev +Conflicts: libcomplearn-dev (<= 1.0.3) +Description: machine-learning through data compression header files + libqsearch is a library for hierarchical tree clustering. Using these + headers, developers can access a wealth of powerful and general techniques + in machine learning and pattern recognition including genomics, optical + character recognition, fuzzy matching, music recognition, and much more + +Package: libqsearch-dev +Section: libdevel +Architecture: any +Depends: libqsearch1 (= ${binary:Version}), libgsl0-dev, pkg-config, libqsearch1-headers (= ${binary:Version}) +Description: nondeterministic quartet tree search library for unrooted trees + qsearch is a library for universal hierarchical clustering using an arbitrary + distance matrix as input. It searches through the space of all possible + unrooted trees of a given size and finds the closest match based on a + weighted quartet cost function determined by the distance matrix. When + used in combination with other feature extraction libraries such as + libcomplearn this system can be used for fast and accurate phylogenetic + reconstruction, linguistic analysis, or stemmatology. + +Package: libqsearch-gomp1 +Architecture: any +Depends: libgomp1, ${shlibs:Depends}, ${misc:Depends} +Conflicts: libcomplearn0, complearn-gui (<= 0.9.8), complearn-mpi (<= 0.9.8) +Description: machine-learning core library runtime files with OpenMP (libgomp) + complearn makes artificial intelligence easy and fast on multi-core + microprocessors. By using the powerful statistical analysis already built + within data compression programs, this library delivers high-quality results + with very low effort + +Package: libqsearch1 +Architecture: any +Conflicts: libcomplearn0 +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: quartet tree search library for hierarchical clustering + Using a distance matrix as input, the qsearch library finds a tree + that fits the input data as well as possible and returns this tree + along with a confidence score for any non-degenerate distance matrix. + +Package: qsearch-tools +Section: science +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: qsearch machine-learning command-line utilities + The tools in this package allow the user to read text, Nexus, or + CompLearn-Binary format files and search for trees that match. The + best tree is determined using a quartet tree scoring system in the + surprisingly simple maketree command. --- libqsearch-1.0.8.orig/debian/libqsearch-gomp-dev.install +++ libqsearch-1.0.8/debian/libqsearch-gomp-dev.install @@ -0,0 +1,3 @@ +debian/libqsearch-gomp/usr/lib/pkgconfig/qsearch-gomp.pc usr/lib/pkgconfig +debian/libqsearch-gomp/usr/lib/libqsearch-gomp.so usr/lib +debian/libqsearch-gomp/usr/lib/libqsearch-gomp.a usr/lib --- libqsearch-1.0.8.orig/debian/libqsearch1.manpages +++ libqsearch-1.0.8/debian/libqsearch1.manpages @@ -0,0 +1 @@ +debian/libqsearch/usr/share/man/man1/qsearch-config.1 --- libqsearch-1.0.8.orig/debian/watch +++ libqsearch-1.0.8/debian/watch @@ -0,0 +1,2 @@ +version=3 +http://complearn.org/download.html .*/libqsearch-(.*)\.tar\.gz --- libqsearch-1.0.8.orig/debian/libqsearch1.install +++ libqsearch-1.0.8/debian/libqsearch1.install @@ -0,0 +1,2 @@ +debian/libqsearch/usr/lib/libqsearch.so.* usr/lib +debian/libqsearch/usr/bin/qsearch-config usr/bin --- libqsearch-1.0.8.orig/debian/libqsearch-gomp1.docs +++ libqsearch-1.0.8/debian/libqsearch-gomp1.docs @@ -0,0 +1,4 @@ +NEWS +README +AUTHORS +THANKS --- libqsearch-1.0.8.orig/debian/rules +++ libqsearch-1.0.8/debian/rules @@ -0,0 +1,62 @@ +#!/usr/bin/make -f +# This file is public domain software, originally written by Joey Hess. + +#export DH_VERBOSE=1 + +build: build-stamp +build-stamp: + dh_testdir + + # Add here commands to compile the package. + mkdir debian/libqsearch + mkdir debian/libqsearch-gomp + cd debian/libqsearch && ../../configure --enable-openmp=no --prefix=/usr && $(MAKE) + cd debian/libqsearch-gomp && ../../configure --enable-openmp=yes --prefix=/usr && $(MAKE) + touch build-stamp + +clean: + dh_testdir + dh_testroot + rm -f build-stamp + + # Add here commands to clean up after the build process. + rm -rf debian/libqsearch debian/libqsearch-gomp + + dh_clean + +install: build + dh_testdir + dh_testroot + dh_clean + dh_installdirs + + # Add here commands to install the package into debian/ + cd debian/libqsearch && $(MAKE) DESTDIR=`pwd` install install-man + cd debian/libqsearch-gomp && $(MAKE) DESTDIR=`pwd` install + +# Build architecture-independent files here. +binary-indep: build install +# We have nothing to do by default. + +# Build architecture-dependent files here. +binary-arch: build install + dh_testdir + dh_testroot + dh_installchangelogs --exclude=ChangeLog + dh_installdocs + dh_installexamples + dh_install + dh_installman + dh_link + dh_strip + dh_compress + dh_fixperms + dh_makeshlibs + dh_installdeb + dh_shlibdeps + dh_gencontrol + dh_md5sums + dh_builddeb + +binary: binary-indep binary-arch +.PHONY: build clean binary-indep binary-arch binary install --- libqsearch-1.0.8.orig/debian/libqsearch-dev.docs +++ libqsearch-1.0.8/debian/libqsearch-dev.docs @@ -0,0 +1,4 @@ +NEWS +README +AUTHORS +THANKS --- libqsearch-1.0.8.orig/debian/qsearch-tools.install +++ libqsearch-1.0.8/debian/qsearch-tools.install @@ -0,0 +1 @@ +debian/libqsearch-gomp/usr/bin/maketree usr/bin/ --- libqsearch-1.0.8.orig/debian/libqsearch1.docs +++ libqsearch-1.0.8/debian/libqsearch1.docs @@ -0,0 +1,4 @@ +NEWS +README +AUTHORS +THANKS --- libqsearch-1.0.8.orig/debian/libqsearch-dev.install +++ libqsearch-1.0.8/debian/libqsearch-dev.install @@ -0,0 +1,4 @@ +debian/libqsearch/usr/lib/pkgconfig/qsearch.pc usr/lib/pkgconfig +debian/libqsearch/usr/share/aclocal/qsearch.m4 usr/share/aclocal +debian/libqsearch/usr/lib/libqsearch.so usr/lib +debian/libqsearch/usr/lib/libqsearch.a usr/lib --- libqsearch-1.0.8.orig/debian/libqsearch-gomp1.install +++ libqsearch-1.0.8/debian/libqsearch-gomp1.install @@ -0,0 +1 @@ +debian/libqsearch-gomp/usr/lib/libqsearch-gomp.so.* usr/lib --- libqsearch-1.0.8.orig/debian/libqsearch1-headers.install +++ libqsearch-1.0.8/debian/libqsearch1-headers.install @@ -0,0 +1,2 @@ +debian/libqsearch/usr/include/qsearch-1.0/qsearch/*.h usr/include/qsearch-1.0/qsearch +debian/libqsearch/usr/include/qsearch-1.0/qsearch.h usr/include/qsearch-1.0 --- libqsearch-1.0.8.orig/debian/libcomplearn-gomp-dev.install +++ libqsearch-1.0.8/debian/libcomplearn-gomp-dev.install @@ -0,0 +1,3 @@ +debian/libqsearch-gomp/usr/lib/pkgconfig/qsearch-gomp.pc usr/lib/pkgconfig +debian/libqsearch-gomp/usr/lib/libqsearch-gomp.so usr/lib +debian/libqsearch-gomp/usr/lib/libqsearch-gomp.a usr/lib --- libqsearch-1.0.8.orig/debian/changelog +++ libqsearch-1.0.8/debian/changelog @@ -0,0 +1,100 @@ +libqsearch (1.0.8-3) unstable; urgency=low + + * Do not put headers into libqsearch-gomp-dev package + Closes: #549637 + * Turn libqsearch1-headers (= ${source:Version}) into + libqsearch1-headers (= ${binary:Version}) to be safe + and trade of between lintian error weak-library-dev-dependency + against not-binnmuable-any-depends-all. IMHO it is more important + to be sure that package versions fit correctly than enabling + binnmus. I did not (yet) created a lintian override to not + hide this issue + + -- Andreas Tille Mon, 05 Oct 2009 13:22:51 +0200 + +libqsearch (1.0.8-2) unstable; urgency=low + + * debian/control: + - Group maintenance in Debian Science Maintainers Team + - Vcs-Svn / Vcs-Browser + - Added myself as Uploaders + - Standards-Version: 3.8.3 (no changes needed) + - debhelper 7 + - Removed explicite dependency from gcc-4.2 + Closes: ##533784 + - do not duplicate Section field if not necessary + - Added versioned depends (= ${binary:Version}) to -dev + packages to comply with policy section 8.5 + * libqsearch-gomp-dev.install: Package libqsearch-gomp-dev + was originally only containing the docs + + -- Andreas Tille Thu, 01 Oct 2009 12:02:38 +0200 + +libqsearch (1.0.8-1) unstable; urgency=low + + * New upstream release. Fixes bug related to new NCD matrix. + + -- Rudi Cilibrasi Mon, 18 Feb 2008 09:22:20 -0800 + +libqsearch (1.0.7-2) unstable; urgency=low + + * Added libgomp1 to Depends because for some reason ${shlibs:Depends} does + not seem to be including it in libqsearch-gomp1. (Closes: #464080) + + -- Rudi Cilibrasi Mon, 04 Feb 2008 19:28:41 -0800 + +libqsearch (1.0.7-1) unstable; urgency=low + + * New upstream release. + + -- Rudi Cilibrasi Thu, 10 Jan 2008 19:35:58 -0800 + +libqsearch (1.0.6-1) unstable; urgency=low + + * New upstream release. + + * Added watch file. + + -- Rudi Cilibrasi Thu, 27 Dec 2007 11:07:42 -0800 + +libqsearch (1.0.5-1) unstable; urgency=low + + * New upstream release, fixing tree-writing bug on 64-bit architectures. + * This initial release closes: #425278. + + -- Rudi Cilibrasi Fri, 02 Nov 2007 14:51:09 -0700 + +libqsearch (1.0.4-1) unstable; urgency=low + + * New upstream release. + * Split into gomp and non-gomp library and dev packages. + + -- Rudi Cilibrasi Tue, 30 Oct 2007 07:47:23 -0700 + +libqsearch (1.0.3-1) unstable; urgency=low + + * New upstream version. + + -- Rudi Cilibrasi Sat, 29 Sep 2007 19:40:14 -0700 + +libqsearch (1.0.1-1) unstable; urgency=low + + * New upstream release. + * Clarified licensing. + + -- Rudi Cilibrasi Sat, 21 Jul 2007 20:26:20 +0200 + +libqsearch (1.0.0-1) unstable; urgency=low + + * New upstream release. + + -- Rudi Cilibrasi Sun, 24 Jun 2007 21:56:13 +0200 + +libqsearch (0.9.9-1) unstable; urgency=low + + * Split tree building from the rest of libcomplearn library to create + this new libqsearch package. Thus, this is the initial release. + * Thanks to Michael Koch for help in packaging. + + -- Rudi Cilibrasi Thu, 10 May 2007 10:21:30 +0200 + --- libqsearch-1.0.8.orig/debian/qsearch-tools.docs +++ libqsearch-1.0.8/debian/qsearch-tools.docs @@ -0,0 +1,3 @@ +NEWS +README +AUTHORS --- libqsearch-1.0.8.orig/debian/copyright +++ libqsearch-1.0.8/debian/copyright @@ -0,0 +1,40 @@ +This package was debianized by Rudi Cilibrasi on +Thu, 10 May 2007 10:16:32 +0200. + +It was downloaded from: http://complearn.org/ + +Upstream Authors: Rudi Cilibrasi + +Copyright: 2003 - 2007 Rudi Cilibrasi + +All rights reserved. + +The Debian packaging is available under the same BSD-like license as the rest +of the source code. + +License: + + 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 the name of the software 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 RULERS 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 RULERS 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. + --- libqsearch-1.0.8.orig/debian/qsearch-tools.manpages +++ libqsearch-1.0.8/debian/qsearch-tools.manpages @@ -0,0 +1 @@ +debian/libqsearch/usr/share/man/man1/maketree.1