Author: plessy Date: 2012-03-30 10:34:48 +0000 (Fri, 30 Mar 2012) New Revision: 10188
Added: trunk/packages/wise/tags/2.4.1-10/ trunk/packages/wise/tags/2.4.1-10/debian/changelog trunk/packages/wise/tags/2.4.1-10/debian/control trunk/packages/wise/tags/2.4.1-10/debian/copyright trunk/packages/wise/tags/2.4.1-10/debian/rules trunk/packages/wise/tags/2.4.1-10/debian/upstream Removed: trunk/packages/wise/tags/2.4.1-10/debian/changelog trunk/packages/wise/tags/2.4.1-10/debian/control trunk/packages/wise/tags/2.4.1-10/debian/copyright trunk/packages/wise/tags/2.4.1-10/debian/rules Log: [svn-buildpackage] Tagging wise 2.4.1-10 Deleted: trunk/packages/wise/tags/2.4.1-10/debian/changelog =================================================================== --- trunk/packages/wise/trunk/debian/changelog 2012-03-30 08:48:02 UTC (rev 10181) +++ trunk/packages/wise/tags/2.4.1-10/debian/changelog 2012-03-30 10:34:48 UTC (rev 10188) @@ -1,146 +0,0 @@ -wise (2.4.1-9) unstable; urgency=low - - * Correct src/models/makefile to link --as-needed (Closes: #641333). - * Conforms with Policy 3.9.2 (debian/control, no other changes needed). - * Corrected VCS URLs (debian/control). - * Use Debhelper 8 (debian/compat, debian/control). - * Added build-arch and build-indep targets to debian/rules. - * Machine-readable debian/copryight file conforms to DEP 5. - * Compress binary package with xz (debian/rules). - - -- Charles Plessy <[email protected]> Wed, 14 Sep 2011 17:52:32 +0900 - -wise (2.4.1-8) unstable; urgency=low - - * Fixed conflicting definitions of getline(). (Closes: #552821) - * Added README.source. - * Standards version 3.8.3. - * Fixed spelling error in package description. - - -- Philipp Benner <[email protected]> Sat, 31 Oct 2009 21:25:52 +0000 - -wise (2.4.1-7) unstable; urgency=low - - [ Steffen Moeller ] - * Now builds with glib-2. (Closes: #523715). Special thank to Barry deFreese. - * Updated policy to 3.8.1 (no changes required). - * fixed api->API lintian warning. - - [ Charles Plessy ] - * debian/control: - - Added myself to the Uploaders. - - Added ${misc:Depends} to the package dependencies. - - Using Debhelper 7 (also debian/compat). - - Eliminated redundancy between the long descriptions of wise and wise-doc. - * Replaced ‘dh_clean -k’ by ‘dh_prep’ in debian/rules. - - -- Charles Plessy <[email protected]> Mon, 15 Jun 2009 20:49:27 +0900 - -wise (2.4.1-6) unstable; urgency=low - - * Updated policy to 3.8.0 (no changes required). - * wise now suggests wise-doc (downgraded from 'recommends'). - [ Steffen Moeller ] - * Using quilt instead of dpatch. - [ Philipp Benner ] - - -- Philipp Benner <[email protected]> Sun, 25 Jan 2009 22:57:27 +0000 - -wise (2.4.1-5) unstable; urgency=low - - * Removed a bashism in debian/rules (Closes: #478639). - - -- Charles Plessy <[email protected]> Sun, 04 May 2008 15:19:01 +0900 - -wise (2.4.1-4) unstable; urgency=low - - * Changed the doc-base section according to the new policy - [Charles Plessy]. - - -- Philipp Benner <[email protected]> Mon, 31 Mar 2008 10:07:35 +0200 - -wise (2.4.1-3) unstable; urgency=low - - * New maintainer e-mail address. - * debian/control: Added DM-Upload-Allowed: yes. - - -- Philipp Benner <[email protected]> Mon, 14 Jan 2008 18:33:27 +0100 - -wise (2.4.1-2) unstable; urgency=low - - * Using official Vcs-Browser and Vcs-Svn fields (debian/control). - * Moved the Homepage: field out from the package's description - + (Charles Plessy). - * Converted copyright file to machine interpretable format. - * Changed maintainer to Debian-Med Packaging Team. - - -- Philipp Benner <[email protected]> Sun, 02 Dec 2007 16:15:50 +0100 - -wise (2.4.1-1) unstable; urgency=low - - * New upstream release. - - -- Philipp Benner <[email protected]> Sat, 15 Sep 2007 17:18:49 +0200 - -wise (2.4.0-3) unstable; urgency=low - - * Removed debtags from debian/control. - * Updated package description (Closes: #435904). - * Excluded genewise21.eps and genewise6.eps from documentation - + (workaround for a bug in gs-esp). - - -- Philipp Benner <[email protected]> Sun, 05 Aug 2007 20:21:35 +0200 - -wise (2.4.0-2) unstable; urgency=low - - * Converted wise2.tex to a pdflatex compatible latex file - + (workaround for a bug in dvips) - - -- Philipp Benner <[email protected]> Fri, 27 Jul 2007 18:46:33 +0200 - -wise (2.4.0-1) unstable; urgency=low - - * New upstream release (Closes: #431392) - * New dpatch (02_isnumber): src/models/phasemodel.c: replaces isnumber() by isdigit() - * New dpatch (03_doc-nodycache): docs/wise2.tex: minor bugfix - - -- Philipp Benner <[email protected]> Tue, 24 Jul 2007 11:58:36 +0200 - -wise (2.2.0-5) unstable; urgency=low - - * Removed obsolete dependencies (Closes: #422123) - - -- Philipp Benner <[email protected]> Sun, 6 May 2007 22:42:27 +0200 - -wise (2.2.0-4) unstable; urgency=low - - * Adapted debian-med tags - * Uscan support - * Migrating to texlive - * use /bin/sh instead of /bin/csh in src/welcome.csh - - -- Philipp Benner <[email protected]> Tue, 27 Mar 2007 19:29:08 +0200 - -wise (2.2.0-3) unstable; urgency=low - - * package tags - * fixed typos in package description - - -- Philipp Benner <[email protected]> Thu, 21 Sep 2006 14:22:39 +0200 - -wise (2.2.0-2) unstable; urgency=low - - * removed \ref tags from package description - * moved examples to package wise-doc - * fixed typo in README.Debian - * minor changes in debian/control - * fixed typo in package description (Closes: #380451) - * new html documentation - - -- Philipp Benner <[email protected]> Sun, 30 Jul 2006 14:08:20 +0200 - -wise (2.2.0-1) unstable; urgency=low - - * Initial release (Closes: #379604) - - -- Philipp Benner <[email protected]> Sun, 23 Jul 2006 17:29:49 +0200 Copied: trunk/packages/wise/tags/2.4.1-10/debian/changelog (from rev 10187, trunk/packages/wise/trunk/debian/changelog) =================================================================== --- trunk/packages/wise/tags/2.4.1-10/debian/changelog (rev 0) +++ trunk/packages/wise/tags/2.4.1-10/debian/changelog 2012-03-30 10:34:48 UTC (rev 10188) @@ -0,0 +1,158 @@ +wise (2.4.1-10) unstable; urgency=low + + * Convert debian/rules to dh, Closes: #666319, as it restores build flags. + * Verbose debhelper in debian/rules. + * Normalised and upgraded debian/copyright file with ‘cme fix’. + * Pre-Depends on dpkg (>= 1.15.6~) (debian/control). + * Conforms to Debian policy 3.9.3 (debian/control, no other changes needed). + * Convert debian/rules to dh, Closes: #666319, as it restores build flags. + * Documented metadata in debian/upstream. + + -- Charles Plessy <[email protected]> Fri, 30 Mar 2012 19:25:53 +0900 + +wise (2.4.1-9) unstable; urgency=low + + * Correct src/models/makefile to link --as-needed (Closes: #641333). + * Conforms with Policy 3.9.2 (debian/control, no other changes needed). + * Corrected VCS URLs (debian/control). + * Use Debhelper 8 (debian/compat, debian/control). + * Added build-arch and build-indep targets to debian/rules. + * Machine-readable debian/copryight file conforms to DEP 5. + * Compress binary package with xz (debian/rules). + + -- Charles Plessy <[email protected]> Wed, 14 Sep 2011 17:52:32 +0900 + +wise (2.4.1-8) unstable; urgency=low + + * Fixed conflicting definitions of getline(). (Closes: #552821) + * Added README.source. + * Standards version 3.8.3. + * Fixed spelling error in package description. + + -- Philipp Benner <[email protected]> Sat, 31 Oct 2009 21:25:52 +0000 + +wise (2.4.1-7) unstable; urgency=low + + [ Steffen Moeller ] + * Now builds with glib-2. (Closes: #523715). Special thank to Barry deFreese. + * Updated policy to 3.8.1 (no changes required). + * fixed api->API lintian warning. + + [ Charles Plessy ] + * debian/control: + - Added myself to the Uploaders. + - Added ${misc:Depends} to the package dependencies. + - Using Debhelper 7 (also debian/compat). + - Eliminated redundancy between the long descriptions of wise and wise-doc. + * Replaced ‘dh_clean -k’ by ‘dh_prep’ in debian/rules. + + -- Charles Plessy <[email protected]> Mon, 15 Jun 2009 20:49:27 +0900 + +wise (2.4.1-6) unstable; urgency=low + + * Updated policy to 3.8.0 (no changes required). + * wise now suggests wise-doc (downgraded from 'recommends'). + [ Steffen Moeller ] + * Using quilt instead of dpatch. + [ Philipp Benner ] + + -- Philipp Benner <[email protected]> Sun, 25 Jan 2009 22:57:27 +0000 + +wise (2.4.1-5) unstable; urgency=low + + * Removed a bashism in debian/rules (Closes: #478639). + + -- Charles Plessy <[email protected]> Sun, 04 May 2008 15:19:01 +0900 + +wise (2.4.1-4) unstable; urgency=low + + * Changed the doc-base section according to the new policy + [Charles Plessy]. + + -- Philipp Benner <[email protected]> Mon, 31 Mar 2008 10:07:35 +0200 + +wise (2.4.1-3) unstable; urgency=low + + * New maintainer e-mail address. + * debian/control: Added DM-Upload-Allowed: yes. + + -- Philipp Benner <[email protected]> Mon, 14 Jan 2008 18:33:27 +0100 + +wise (2.4.1-2) unstable; urgency=low + + * Using official Vcs-Browser and Vcs-Svn fields (debian/control). + * Moved the Homepage: field out from the package's description + + (Charles Plessy). + * Converted copyright file to machine interpretable format. + * Changed maintainer to Debian-Med Packaging Team. + + -- Philipp Benner <[email protected]> Sun, 02 Dec 2007 16:15:50 +0100 + +wise (2.4.1-1) unstable; urgency=low + + * New upstream release. + + -- Philipp Benner <[email protected]> Sat, 15 Sep 2007 17:18:49 +0200 + +wise (2.4.0-3) unstable; urgency=low + + * Removed debtags from debian/control. + * Updated package description (Closes: #435904). + * Excluded genewise21.eps and genewise6.eps from documentation + + (workaround for a bug in gs-esp). + + -- Philipp Benner <[email protected]> Sun, 05 Aug 2007 20:21:35 +0200 + +wise (2.4.0-2) unstable; urgency=low + + * Converted wise2.tex to a pdflatex compatible latex file + + (workaround for a bug in dvips) + + -- Philipp Benner <[email protected]> Fri, 27 Jul 2007 18:46:33 +0200 + +wise (2.4.0-1) unstable; urgency=low + + * New upstream release (Closes: #431392) + * New dpatch (02_isnumber): src/models/phasemodel.c: replaces isnumber() by isdigit() + * New dpatch (03_doc-nodycache): docs/wise2.tex: minor bugfix + + -- Philipp Benner <[email protected]> Tue, 24 Jul 2007 11:58:36 +0200 + +wise (2.2.0-5) unstable; urgency=low + + * Removed obsolete dependencies (Closes: #422123) + + -- Philipp Benner <[email protected]> Sun, 6 May 2007 22:42:27 +0200 + +wise (2.2.0-4) unstable; urgency=low + + * Adapted debian-med tags + * Uscan support + * Migrating to texlive + * use /bin/sh instead of /bin/csh in src/welcome.csh + + -- Philipp Benner <[email protected]> Tue, 27 Mar 2007 19:29:08 +0200 + +wise (2.2.0-3) unstable; urgency=low + + * package tags + * fixed typos in package description + + -- Philipp Benner <[email protected]> Thu, 21 Sep 2006 14:22:39 +0200 + +wise (2.2.0-2) unstable; urgency=low + + * removed \ref tags from package description + * moved examples to package wise-doc + * fixed typo in README.Debian + * minor changes in debian/control + * fixed typo in package description (Closes: #380451) + * new html documentation + + -- Philipp Benner <[email protected]> Sun, 30 Jul 2006 14:08:20 +0200 + +wise (2.2.0-1) unstable; urgency=low + + * Initial release (Closes: #379604) + + -- Philipp Benner <[email protected]> Sun, 23 Jul 2006 17:29:49 +0200 Deleted: trunk/packages/wise/tags/2.4.1-10/debian/control =================================================================== --- trunk/packages/wise/trunk/debian/control 2012-03-30 08:48:02 UTC (rev 10181) +++ trunk/packages/wise/tags/2.4.1-10/debian/control 2012-03-30 10:34:48 UTC (rev 10188) @@ -1,48 +0,0 @@ -Source: wise -Section: science -Priority: optional -Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Philipp Benner <[email protected]>, Steffen Moeller <[email protected]>, Charles Plessy <[email protected]> -Build-Depends: debhelper (>= 8), quilt, texlive-latex-base, - texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev -Standards-Version: 3.9.2 -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/wise/ -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/wise/trunk/ -Homepage: http://www.ebi.ac.uk/~birney/wise2/ - -Package: wise -Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} -Suggests: wise-doc (= ${source:Version}) -Description: comparison of biopolymers, commonly DNA and protein sequences - Wise2 is a package focused on comparisons of biopolymers, commonly DNA - and protein sequences. There are many other packages which do - this, probably the best known being BLAST package (from NCBI) and the - Fasta package (from Bill Pearson). There are other packages, such as - the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused - on hidden Markov models (HMMs) of biopolymers. - . - Wise2's particular forte is the comparison of DNA sequence at the level - of its protein translation. This comparison allows the simultaneous - prediction of say gene structure with homology based alignment. - . - Wise2 also contains other algorithms, such as the venerable Smith-Waterman - algorithm, or more modern ones such as Stephen Altschul's generalised - gap penalties, or even experimental ones developed in house, such as - dba. The development of these algorithms is due to the ease of developing - such algorithms in the environment used by Wise2. - . - Wise2 has also been written with an eye for reuse and maintainability. - Although it is a pure C package you can access its functionality - directly in Perl. Parts of the package (or the entire package) can - be used by other C or C++ programs without namespace clashes as all - externally linked variables have the unique identifier Wise2 prepended. - -Package: wise-doc -Architecture: all -Section: doc -Depends: ${misc:Depends} -Recommends: wise (= ${source:Version}), xpdf-reader | pdf-viewer -Description: documentation for the wise package - This package contains the documentation for Wise2, a package focused on - comparisons of biopolymers, commonly DNA and protein sequences. Copied: trunk/packages/wise/tags/2.4.1-10/debian/control (from rev 10186, trunk/packages/wise/trunk/debian/control) =================================================================== --- trunk/packages/wise/tags/2.4.1-10/debian/control (rev 0) +++ trunk/packages/wise/tags/2.4.1-10/debian/control 2012-03-30 10:34:48 UTC (rev 10188) @@ -0,0 +1,50 @@ +Source: wise +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Philipp Benner <[email protected]>, Steffen Moeller <[email protected]>, Charles Plessy <[email protected]> +Build-Depends: debhelper (>= 8), quilt, texlive-latex-base, + texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev +Standards-Version: 3.9.3 +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/wise/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/wise/trunk/ +Homepage: http://www.ebi.ac.uk/~birney/wise2/ + +Package: wise +Architecture: any +Pre-Depends: dpkg (>= 1.15.6~) +Depends: ${shlibs:Depends}, ${misc:Depends} +Suggests: wise-doc (= ${source:Version}) +Description: comparison of biopolymers, commonly DNA and protein sequences + Wise2 is a package focused on comparisons of biopolymers, commonly DNA + and protein sequences. There are many other packages which do + this, probably the best known being BLAST package (from NCBI) and the + Fasta package (from Bill Pearson). There are other packages, such as + the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused + on hidden Markov models (HMMs) of biopolymers. + . + Wise2's particular forte is the comparison of DNA sequence at the level + of its protein translation. This comparison allows the simultaneous + prediction of say gene structure with homology based alignment. + . + Wise2 also contains other algorithms, such as the venerable Smith-Waterman + algorithm, or more modern ones such as Stephen Altschul's generalised + gap penalties, or even experimental ones developed in house, such as + dba. The development of these algorithms is due to the ease of developing + such algorithms in the environment used by Wise2. + . + Wise2 has also been written with an eye for reuse and maintainability. + Although it is a pure C package you can access its functionality + directly in Perl. Parts of the package (or the entire package) can + be used by other C or C++ programs without namespace clashes as all + externally linked variables have the unique identifier Wise2 prepended. + +Package: wise-doc +Architecture: all +Section: doc +Pre-Depends: dpkg (>= 1.15.6~) +Depends: ${misc:Depends} +Recommends: wise (= ${source:Version}), xpdf-reader | pdf-viewer +Description: documentation for the wise package + This package contains the documentation for Wise2, a package focused on + comparisons of biopolymers, commonly DNA and protein sequences. Deleted: trunk/packages/wise/tags/2.4.1-10/debian/copyright =================================================================== --- trunk/packages/wise/trunk/debian/copyright 2012-03-30 08:48:02 UTC (rev 10181) +++ trunk/packages/wise/tags/2.4.1-10/debian/copyright 2012-03-30 10:34:48 UTC (rev 10188) @@ -1,86 +0,0 @@ -Format: http://dep.debian.net/deps/dep5/ -Source: http://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz - -Files: * -Copyright: © 1996-2001 Genome Research Limited (GRL) and - Ewan Birney <[email protected]> and Sean Eddy -License: GRL - All of the documentation and software included in the dyc directory of the - Wise2 package directory is copyrighted by Genome Research Limited - (GRL) and other individuals where appropriate. This license is modelled - after the 'BSD' style license and is appropriate for use by both - academic and commercial sites, without placing any restriction on the - distribution of source code from other sources with this software. - . - 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 GRL nor the names of its contributors may be used - to endorse or promote products derived from this software without - specific prior written permission. - . - It is considered polite to indicate where appropriate that software which - is developed using this source code includes a statement that it was developed - using the Wise2 soure code. This is not a requirement however. - . - THIS SOFTWARE IS PROVIDED BY THE GRL 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 GRL 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/HMMer2/* -Copyright: © 1992-1996 Sean R. Eddy -License: GPL-2 - This source code is distributed under the terms of the - GNU General Public License. See the files COPYING and - GNULICENSE for details. - -Files: - src/dynlibsrc/histogram.dy src/dynlibsrc/histogram.pod - src/dynlibsrc/histogram.tex -Copyright: © 1996-1999 Genome Research Limited (GRL) and Sean Eddy -License: LGPL-any - Converted by Ewan Birney to Dynamite source June 98. - Copyright is LGPL. For more info read READMEs -Comment: On Debian GNU/Linux systems, the complete text of the GNU Lesser - General Public License version 3 can be found in `/usr/share/common-licenses/LGPL-3'. - -Files: debian/* -Copyright: © 2006-2007 Philipp Benner <[email protected]> - © 2009 Steffen Moeller <[email protected]> - © 2009 Charles Plessy <[email protected]> - © 2009 Barry deFreese <[email protected]> -License: GPL-2+ - 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 Street, Fifth Floor, Boston, MA 02110-1301 USA. -Comment: On Debian GNU/Linux systems, the complete text of the GNU General Public - License version 2 can be found in `/usr/share/common-licenses/GPL-2' and the - complete text of the GNU Lesser General Public License can be found in - `/usr/share/common-licenses/LGPL-3'. Copied: trunk/packages/wise/tags/2.4.1-10/debian/copyright (from rev 10182, trunk/packages/wise/trunk/debian/copyright) =================================================================== --- trunk/packages/wise/tags/2.4.1-10/debian/copyright (rev 0) +++ trunk/packages/wise/tags/2.4.1-10/debian/copyright 2012-03-30 10:34:48 UTC (rev 10188) @@ -0,0 +1,87 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Source: http://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz + +Files: * +Copyright: © 1996-2001 Genome Research Limited (GRL) and + Ewan Birney <[email protected]> and Sean Eddy +License: GRL + All of the documentation and software included in the dyc directory of the + Wise2 package directory is copyrighted by Genome Research Limited + (GRL) and other individuals where appropriate. This license is modelled + after the 'BSD' style license and is appropriate for use by both + academic and commercial sites, without placing any restriction on the + distribution of source code from other sources with this software. + . + 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 GRL nor the names of its contributors may be used + to endorse or promote products derived from this software without + specific prior written permission. + . + It is considered polite to indicate where appropriate that software which + is developed using this source code includes a statement that it was developed + using the Wise2 soure code. This is not a requirement however. + . + THIS SOFTWARE IS PROVIDED BY THE GRL 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 GRL 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/HMMer2/* +Copyright: © 1992-1996 Sean R. Eddy +License: GPL-2 + This source code is distributed under the terms of the + GNU General Public License. See the files COPYING and + GNULICENSE for details. + +Files: + src/dynlibsrc/histogram.dy src/dynlibsrc/histogram.pod + src/dynlibsrc/histogram.tex +Copyright: © 1996-1999 Genome Research Limited (GRL) and Sean Eddy +License: LGPL-any + Converted by Ewan Birney to Dynamite source June 98. + Copyright is LGPL. For more info read READMEs +Comment: On Debian GNU/Linux systems, the complete text of the GNU Lesser + General Public License version 3 can be found in `/usr/share/common-licenses/LGPL-3'. + +Files: debian/* +Copyright: © 2006-2007 Philipp Benner <[email protected]> + © 2009 Steffen Moeller <[email protected]> + © 2009 Charles Plessy <[email protected]> + © 2009 Barry deFreese <[email protected]> +License: GPL-2+ + 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 Street, Fifth Floor, Boston, MA 02110-1301 USA. +Comment: On Debian GNU/Linux systems, the complete text of the GNU General Public + License version 2 can be found in `/usr/share/common-licenses/GPL-2' and the + complete text of the GNU Lesser General Public License can be found in + `/usr/share/common-licenses/LGPL-3'. + Deleted: trunk/packages/wise/tags/2.4.1-10/debian/rules =================================================================== --- trunk/packages/wise/trunk/debian/rules 2012-03-30 08:48:02 UTC (rev 10181) +++ trunk/packages/wise/tags/2.4.1-10/debian/rules 2012-03-30 10:34:48 UTC (rev 10188) @@ -1,158 +0,0 @@ -#!/usr/bin/make -f -# -*- makefile -*- - -# Uncomment this to turn on verbose mode. -#export DH_VERBOSE=1 - -CFLAGS = -Wall -g - -ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) - CFLAGS += -O0 -else - CFLAGS += -O2 -endif - -include /usr/share/quilt/quilt.make - -configure: configure-stamp -configure-stamp: - dh_testdir - - touch configure-stamp - -build: patch build-stamp -build-stamp: $(QUILT_STAMPFN) configure-stamp build-arch-stamp build-indep-stamp - dh_testdir - touch $@ - -build-arch: build-arch-stamp -build-arch-stamp: - dh_testdir - $(MAKE) -C src all - $(MAKE) -C debian/manpages.d - touch $@ - -build-indep: build-indep-stamp -build-indep-stamp: - dh_testdir - -# build documentation manually (docs/makefile is not useable) - cat src/models/*.tex src/dynlibsrc/*.tex | perl docs/gettex.pl > docs/temp.tex - cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex -# <bugfix> - sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex - sed -i 's/label{module_sequence\\_codon}/label{module_sequence_codon}/' docs/api.tex - sed -i 's/Wise2::GeneParameter21_wrap/Wise2::GeneParameter21\\_wrap/' docs/api.tex -# </bugfix> - cd docs && pdflatex api.tex - cd docs && pdflatex api.tex - cd docs && pdflatex dynamite.tex - cd docs && pdflatex dynamite.tex -# cd docs && ps2pdf genewise6.eps # segfaults on s390 -# cd docs && ps2pdf genewise21.eps - cd docs && pdflatex wise2.tex - cd docs && pdflatex wise2.tex - - cd docs && hevea api.tex - cd docs && hevea api.tex - cd docs && hevea dynamite.tex - cd docs && hevea dynamite.tex - cd docs && hevea wise2.tex - cd docs && hevea wise2.tex - - mkdir -p docs/api - mkdir -p docs/dynamite - mkdir -p docs/wise2 - - mv docs/api.html docs/api - mv docs/dynamite.html docs/dynamite - mv docs/wise2.html docs/wise2 - - touch $@ - -clean: unpatch - dh_testdir - dh_testroot - rm -f build-stamp configure-stamp - - $(MAKE) -C src clean - $(MAKE) -C debian/manpages.d clean - -# bugfix - $(RM) -r src/oldbin - for i in dba psw dnal genomewise pswdb scanwise estwise genewise sywise genewisedb promoterwise pseudowise estwisedb; do $(RM) src/modules/$$i; done - $(RM) src/network/scanwise_server - -# clean documentation - $(RM) docs/temp.tex - $(RM) docs/api.* - $(RM) docs/wise2.image.tex - $(RM) docs/*.pdf - $(RM) docs/*.aux - $(RM) docs/*.log - $(RM) docs/*.toc - $(RM) docs/*.pdf - $(RM) docs/*.dvi - $(RM) docs/*.ps - $(RM) docs/*.4ct - $(RM) docs/*.4tc - $(RM) docs/*.css - $(RM) docs/*.idv - $(RM) docs/*.lg - $(RM) docs/*.tmp - $(RM) docs/*.xref - $(RM) docs/*.haux - $(RM) docs/*.htoc - $(RM) docs/*.html - - $(RM) -r docs/api - $(RM) -r docs/dynamite - $(RM) -r docs/wise2 - - dh_clean - -install: build - dh_testdir - dh_testroot - dh_prep - dh_installdirs - -# $(MAKE) install DESTDIR=$(CURDIR)/debian/wise - install -m 755 src/bin/* debian/wise/usr/bin - install -m 755 src/models/genomewise debian/wise/usr/bin - -binary-indep: build install - dh_testdir -i - dh_testroot -i - dh_installchangelogs -i - dh_installdocs -i - dh_installexamples -i - dh_installman -i - dh_link -i - dh_strip -i - dh_compress -i - dh_fixperms -i - dh_installdeb -i - dh_gencontrol -i - dh_md5sums -i - dh_builddeb -i -- -Z xz - -binary-arch: build install - dh_testdir -a - dh_testroot -a - dh_installchangelogs -a - dh_installdocs -a - dh_installexamples -a - dh_installman -a - dh_link -a - dh_strip -a - dh_compress -a - dh_fixperms -a - dh_installdeb -a - dh_shlibdeps -a - dh_gencontrol -a - dh_md5sums -a - dh_builddeb -a -- -Z xz - -binary: binary-indep binary-arch -.PHONY: build build-arch build-indep clean binary-indep binary-arch binary install configure Copied: trunk/packages/wise/tags/2.4.1-10/debian/rules (from rev 10184, trunk/packages/wise/trunk/debian/rules) =================================================================== --- trunk/packages/wise/tags/2.4.1-10/debian/rules (rev 0) +++ trunk/packages/wise/tags/2.4.1-10/debian/rules 2012-03-30 10:34:48 UTC (rev 10188) @@ -0,0 +1,82 @@ +#!/usr/bin/make -f +# -*- makefile -*- + +# Uncomment this to turn on verbose mode. +export DH_VERBOSE=1 + +%: + dh $@ --with quilt + +override_dh_auto_build: + $(MAKE) -C src all + $(MAKE) -C debian/manpages.d +# build documentation manually (docs/makefile is not useable) + cat src/models/*.tex src/dynlibsrc/*.tex | perl docs/gettex.pl > docs/temp.tex + cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex +# <bugfix> + sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex + sed -i 's/label{module_sequence\\_codon}/label{module_sequence_codon}/' docs/api.tex + sed -i 's/Wise2::GeneParameter21_wrap/Wise2::GeneParameter21\\_wrap/' docs/api.tex +# </bugfix> + cd docs && pdflatex api.tex + cd docs && pdflatex api.tex + cd docs && pdflatex dynamite.tex + cd docs && pdflatex dynamite.tex +# cd docs && ps2pdf genewise6.eps # segfaults on s390 +# cd docs && ps2pdf genewise21.eps + cd docs && pdflatex wise2.tex + cd docs && pdflatex wise2.tex + cd docs && hevea api.tex + cd docs && hevea api.tex + cd docs && hevea dynamite.tex + cd docs && hevea dynamite.tex + cd docs && hevea wise2.tex + cd docs && hevea wise2.tex + mkdir -p docs/api + mkdir -p docs/dynamite + mkdir -p docs/wise2 + mv docs/api.html docs/api + mv docs/dynamite.html docs/dynamite + mv docs/wise2.html docs/wise2 + touch $@ + +override_dh_clean: + $(MAKE) -C src clean + $(MAKE) -C debian/manpages.d clean +# bugfix + $(RM) -r src/oldbin + for i in dba psw dnal genomewise pswdb scanwise estwise genewise sywise genewisedb promoterwise pseudowise estwisedb; do $(RM) src/modules/$$i; done + $(RM) src/network/scanwise_server +# clean documentation + $(RM) docs/temp.tex + $(RM) docs/api.* + $(RM) docs/wise2.image.tex + $(RM) docs/*.pdf + $(RM) docs/*.aux + $(RM) docs/*.log + $(RM) docs/*.toc + $(RM) docs/*.pdf + $(RM) docs/*.dvi + $(RM) docs/*.ps + $(RM) docs/*.4ct + $(RM) docs/*.4tc + $(RM) docs/*.css + $(RM) docs/*.idv + $(RM) docs/*.lg + $(RM) docs/*.tmp + $(RM) docs/*.xref + $(RM) docs/*.haux + $(RM) docs/*.htoc + $(RM) docs/*.html + $(RM) -r docs/api + $(RM) -r docs/dynamite + $(RM) -r docs/wise2 + dh_clean + +override_dh_install: +# $(MAKE) install DESTDIR=$(CURDIR)/debian/wise + install -m 755 src/bin/* debian/wise/usr/bin + install -m 755 src/models/genomewise debian/wise/usr/bin + +override_dh_builddeb: + dh_builddeb -- -Z xz Copied: trunk/packages/wise/tags/2.4.1-10/debian/upstream (from rev 10185, trunk/packages/wise/trunk/debian/upstream) =================================================================== --- trunk/packages/wise/tags/2.4.1-10/debian/upstream (rev 0) +++ trunk/packages/wise/tags/2.4.1-10/debian/upstream 2012-03-30 10:34:48 UTC (rev 10188) @@ -0,0 +1,7 @@ +Homepage: http://www.ebi.ac.uk/~birney/wise2/ +Name: Wise2 +Watch: | + version=3 + http://www.ebi.ac.uk/~birney/wise2/ (?:./)?wise(.*)\.tar\.gz \ + debian uupdate +Webservice: http://www.ebi.ac.uk/Tools/Wise2/ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
