theseus (3.3.0-8) unstable; urgency=medium * Fix string buffer size Closes: #908459 -- Andreas Tille Wed, 10 Oct 2018 08:04:34 +0200 theseus (3.3.0-7) unstable; urgency=medium [ Fabian Kloetzl ] * Team upload. * Fix string bugs uncovered by gcc8 Closes: #908459 [ Andreas Tille ] * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 -- Fabian Kloetzl Mon, 10 Sep 2018 09:56:01 +0000 theseus (3.3.0-6) unstable; urgency=medium * Move packaging from SVN to Git * debhelper 10 * Standards-Version: 4.1.0 (no changes needed) * Use DEB_SOURCE in d/rules * Increase string length of string buffer to build with gcc-7 Closes: #853681 * Hardening -- Andreas Tille Thu, 24 Aug 2017 15:31:38 +0200 theseus (3.3.0-5) unstable; urgency=medium * Depends: muscle instead of Suggests since its usage in test suite seems to make this sensible. * cme fix dpkg-control * Remove Morten Kjeldgaard from uploaders who did not committed for 8 years * Better hardening -- Andreas Tille Fri, 29 Apr 2016 13:29:14 +0200 theseus (3.3.0-4) unstable; urgency=medium * Enable building arch independent packages separately Closes: #806223 * Build against libgsl-dev (version 2) rather than libgsl0-dev * Add autopkgtest -- Andreas Tille Wed, 25 Nov 2015 18:01:44 +0100 theseus (3.3.0-3) unstable; urgency=medium * Fix versioning which really Closes: #790515 -- Andreas Tille Tue, 07 Jul 2015 09:03:03 +0200 theseus (3.3.0-2) unstable; urgency=medium * Fix package split issue Closes: #790515 -- Andreas Tille Wed, 01 Jul 2015 10:12:21 +0200 theseus (3.3.0-1) unstable; urgency=medium * New upstream version * Add missing license statement Closes: #790311 -- Andreas Tille Sun, 28 Jun 2015 15:04:59 +0200 theseus (3.1.1-1) unstable; urgency=medium * New upstream version * cme fix dpkg-control * Split examples into separate binary package * update debian/copyright -- Andreas Tille Thu, 21 May 2015 16:53:46 +0200 theseus (3.0.0-1) unstable; urgency=medium * New upstream version * Moved debian/upstream to debian/upstream/metadata * cme fix dpkg-control * debian/README.source: removed since redundant -- Andreas Tille Tue, 20 May 2014 15:08:38 +0200 theseus (2.0.6-1) unstable; urgency=low * New upstream version - Adapt patches - debian/patches/30_fix_gcc_options.patch: Enable build on Linux Closes: #713461 * debian/control: - Remove DM-Upload-Allowed - cme fix dpkg-control * debian/rules: use xz compression -- Andreas Tille Wed, 26 Jun 2013 16:34:53 +0200 theseus (2.0.1-1) experimental; urgency=low * New upstream version (most patches applied) * debian/control: - Fix typo: s/clustlaw/clustalw/ Closes: #682994 - Standards-Version: 3.9.4 (no changes needed) * removed debian/citation.bib because the very same information is now in debian/upstream -- Andreas Tille Thu, 11 Oct 2012 18:15:43 +0200 theseus (1.6.2-2) unstable; urgency=low * debian/upstream: Added missing space, fixed Name * debian/patches: Two patches from Simon Ruderich to enable hardening (thanks to Simon) Closes: #668120 -- Andreas Tille Fri, 08 Jun 2012 08:45:38 +0200 theseus (1.6.2-1) unstable; urgency=low * New upstream version (adapted patch) * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs fields * debian/{control,rules}: Do not mention quilt explicitly which is not needed with source version 3.0 (quilt) * debian/upstream: Use information from debian/citation.bib for References in upstream yaml format * debian/upstream: Use information from debian/citation.bib for References in upstream yaml format * debian/{control,compat}: debhelper 9 to enable hardening flags * debian/patches/20_hardening.patch: Enable building with hardening options * debian/patches/20_exclude_apple_options.patch: Prevent trying to link with Apple specific linker option and enable linking pthread * debian/copyright: Rewritten to match DEP5 and verified using cme fix dpkg-copyright -- Andreas Tille Sat, 24 Mar 2012 07:48:57 +0100 theseus (1.6.1-1) unstable; urgency=low * New upstream version * debian/patches: - 99-theseus_align.sh.patch: Replaced by sed script in debian/rules which works (hopefully) for future versions as well without manually changing the patch - use_muscle_instead_of_clustalw.patch: Removed because clustalw is no in main and we do not need to actively replace it by muscle - 00-makefile.patch: Removed because applied upstream - 200-make.inc.patch: Removed + One purpose was to replace not working libtool call by ar which was applied upstream + Other purpose was to enable liblapack (patch by Morten Kjeldgaard) which was discussed with upstream and seems to cause problems. So it was deactivated for now and might be tested later for enabling higher performance if needed. -- Andreas Tille Wed, 26 Jan 2011 11:39:36 +0100 theseus (1.5.5-1) unstable; urgency=low * New upstream version * Standards-Version: 3.9.1 (no changes needed) * Adapt debian/patches to new upstream version * Source format 3.0 (quilt) * debian/patches/use_muscle_instead_of_clustalw.patch: The script thesaus_align says it would use muscle as align program but it actually uses clustalw which is in non-free and thus we can not recommend it. The patch makes muscle really the default * Depends: muscle (instead of Suggests) * debian/theseus_align.1: Better wording for muscle preference -- Andreas Tille Wed, 24 Nov 2010 17:46:49 +0100 theseus (1.4.3-2) unstable; urgency=low * debian/patches/10_kbsd.patch: Correctly applied patch from Cyril (sorry for mixing this up) Closes: #542879 -- Andreas Tille Thu, 03 Sep 2009 08:49:22 +0200 theseus (1.4.3-1) unstable; urgency=low [Andreas Tille] * New upstream version Closes: #534630 * debian/control - Added myself to uploaders - debhelper 7 - Build-Depends: libtool - Standards-Version: 3.8.3 (no changes needed) * Switched to quilt (affects debian/patches/*, debian/control, debian/rules) * Added Suggests: clustlaw, mafft, t-coffee, kalign, dialign because these are called in theseus_align * Use debian/{docs,manpages, examples} instead of arguments of the debhelper installers to enable short rules file * Re-enabled patch for theseus_align and do not tweak upstream tarball just to s?usr/local/bin?usr/bin? * debian/patches/200-make.inc.patch: Use ar directly to to avoid problems with libtool, drop -arch command line options to gcc which let compilation fail * debian/README.Debian: Removed paragraph about theseus_align because this is now shipped in upstream tarball * debian/patches/10_kbsd.patch: fix the FTBFS problem reported by Cyril Brulebois (thanks to Cyril for the patch) Closes: #542879 [Morten Kjeldgaard] * Fix FTBFS on certain platforms that lack the Atlas libraries by using lapack-dev in Build-Depends. This will pull in Atlas on the relevant platforms, otherwise not. -- Andreas Tille Mon, 31 Aug 2009 14:50:19 +0200 theseus (1.3.9-1) unstable; urgency=low * New upstream release, first upload to Debian. -- Morten Kjeldgaard Sun, 16 Nov 2008 22:36:36 +0100 theseus (1.1.5-0ubuntu3) intrepid; urgency=low * gfortran transition for intrepid, atlas3-base -> libatlas3-base. -- Morten Kjeldgaard Thu, 04 Sep 2008 23:20:52 +0200 theseus (1.1.5-0ubuntu2) hardy; urgency=low * debian/rules: FTBFS on all archs but i386, due to missing binary-arch target (LP: #181359) * Removed redundant libraries. -- Morten Kjeldgaard Tue, 08 Jan 2008 22:35:42 +0100 theseus (1.1.5-0ubuntu1) hardy; urgency=low * Initial release (LP: #173506) * The upstream tarball has been versioned as 1.1.5 (not versioned upstream) The get-orig-source target in debian/rules can be used for this purpose once the changelog has been edited to contain the right version * Patch to theseus.1 and theseus_align.1 - fix incorrect .TH line in theseus.1 - fix multiple instances of hyphen (-) to minus (\-) * Patch on thesus_align.sh. The script is patched to find programs in /usr/bin. The script makes use of the multiple sequence alignment program muscle, which is available from universe. * Patch make.inc to provide correct compiler switches. * A script (getexamples) is provided to show the user how (s)he can download the data in examples/ -- Morten Kjeldgaard Sun, 02 Dec 2007 15:53:15 +0100