theseus (3.3.0-14) unstable; urgency=medium
* Building theseus only on amd64 and i386, see Bug #1017563
* Adding myself as uploader
-- Pierre Gruet <pgt@debian.org> Fri, 18 Nov 2022 18:15:57 +0100
theseus (3.3.0-13) unstable; urgency=medium
* Restoring the d/dirs file
-- Pierre Gruet <pgt@debian.org> Wed, 17 Aug 2022 08:07:24 +0200
theseus (3.3.0-12) unstable; urgency=medium
* Team upload
* Removing unused linefix function, which returns a resource just after
releasing it (Closes: #1017325)
* Raising Standards version to 4.6.1 (no change)
* Removing now useless debian/dirs file
* Updating d/watch URI, which is now secure
-- Pierre Gruet <pgt@debian.org> Tue, 16 Aug 2022 22:25:07 +0200
theseus (3.3.0-11) unstable; urgency=medium
* Adapt theseus_align to muscle version 5
Closes: #1004506
-- Andreas Tille <tille@debian.org> Sun, 30 Jan 2022 17:18:29 +0100
theseus (3.3.0-10) unstable; urgency=medium
* Fix watch file
* Standards-Version: 4.6.0 (routine-update)
* Apply multi-arch hints.
+ theseus-examples: Add Multi-Arch: foreign.
-- Andreas Tille <tille@debian.org> Thu, 30 Sep 2021 11:50:04 +0200
theseus (3.3.0-9) unstable; urgency=medium
* Standards-Version: 4.5.1 (routine-update)
* debhelper-compat 13 (routine-update)
* Secure URI in copyright format (routine-update)
* Remove trailing whitespace in debian/changelog (routine-update)
* Remove trailing whitespace in debian/copyright (routine-update)
* autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Update watch file format version to 4.
* Refer to specific version of license GPL-3+.
* Remove obsolete field Name from debian/upstream/metadata (already present in
machine-readable debian/copyright).
-- Andreas Tille <tille@debian.org> Tue, 24 Nov 2020 15:49:14 +0100
theseus (3.3.0-8) unstable; urgency=medium
* Fix string buffer size
Closes: #908459
-- Andreas Tille <tille@debian.org> 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 <kloetzl@evolbio.mpg.de> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> Wed, 25 Nov 2015 18:01:44 +0100
theseus (3.3.0-3) unstable; urgency=medium
* Fix versioning which really
Closes: #790515
-- Andreas Tille <tille@debian.org> Tue, 07 Jul 2015 09:03:03 +0200
theseus (3.3.0-2) unstable; urgency=medium
* Fix package split issue
Closes: #790515
-- Andreas Tille <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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
<simon@ruderich.org> to enable hardening (thanks to Simon)
Closes: #668120
-- Andreas Tille <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <kibi@debian.org> (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 <tille@debian.org> 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 <mok0@ubuntu.com> 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 <mok0@ubuntu.com> 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 <mok@bioxray.dk> 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 <mok@bioxray.dk> Sun, 02 Dec 2007 15:53:15 +0100