Change log for theseus package in Ubuntu

theseus (3.3.0-14) unstable; urgency=medium

  * Building theseus only on amd64 and i386, see Bug #1017563
  * Adding myself as uploader

 -- Pierre Gruet <email address hidden>  Fri, 18 Nov 2022 18:15:57 +0100

Available diffs

• diff from 3.3.0-11 to 3.3.0-14 (1.7 KiB)
• diff from 3.3.0-13 to 3.3.0-14 (602 bytes)

theseus (3.3.0-13) unstable; urgency=medium

  * Restoring the d/dirs file

 -- Pierre Gruet <email address hidden>  Wed, 17 Aug 2022 08:07:24 +0200

Available diffs

• diff from 3.3.0-12 to 3.3.0-13 (327 bytes)

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 <email address hidden>  Tue, 16 Aug 2022 22:25:07 +0200

Available diffs

• diff from 3.3.0-11 to 3.3.0-12 (1.5 KiB)

theseus (3.3.0-11) unstable; urgency=medium

  * Adapt theseus_align to muscle version 5
    Closes: #1004506

 -- Andreas Tille <email address hidden>  Sun, 30 Jan 2022 17:18:29 +0100

Available diffs

• diff from 3.3.0-10build1 (in Ubuntu) to 3.3.0-11 (1.1 KiB)

theseus (3.3.0-10build1) jammy; urgency=medium

  * No-change rebuild against libgsl27

 -- Steve Langasek <email address hidden>  Tue, 07 Dec 2021 17:44:00 +0000

Available diffs

• diff from 3.3.0-10 (in Debian) to 3.3.0-10build1 (492 bytes)

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 <email address hidden>  Thu, 30 Sep 2021 11:50:04 +0200

Available diffs

• diff from 3.3.0-9 to 3.3.0-10 (734 bytes)

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 <email address hidden>  Tue, 24 Nov 2020 15:49:14 +0100

Available diffs

• diff from 3.3.0-8build1 (in Ubuntu) to 3.3.0-9 (2.1 KiB)

theseus (3.3.0-8build1) groovy; urgency=medium

  * No-change rebuild against libgsl25

 -- Graham Inggs <email address hidden>  Thu, 07 May 2020 22:25:50 +0000

Available diffs

• diff from 3.3.0-8 (in Debian) to 3.3.0-8build1 (306 bytes)

theseus (3.3.0-8) unstable; urgency=medium

  * Fix string buffer size
    Closes: #908459

 -- Andreas Tille <email address hidden>  Wed, 10 Oct 2018 08:04:34 +0200

Available diffs

• diff from 3.3.0-6 to 3.3.0-8 (8.0 KiB)
• diff from 3.3.0-7 to 3.3.0-8 (869 bytes)

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 <email address hidden>  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 <email address hidden>  Thu, 24 Aug 2017 15:31:38 +0200

Available diffs

• diff from 3.3.0-5ubuntu1 (in Ubuntu) to 3.3.0-6 (2.2 KiB)

theseus (3.3.0-5ubuntu1) artful; urgency=medium

  * Build with -Wno-error=format-overflow to build with GCC 7.

 -- Matthias Klose <email address hidden>  Sun, 06 Aug 2017 13:48:51 +0000

Available diffs

• diff from 3.3.0-5 (in Debian) to 3.3.0-5ubuntu1 (634 bytes)
• diff from 3.3.0-5build1 to 3.3.0-5ubuntu1 (630 bytes)

theseus (3.3.0-5build1) artful; urgency=medium

  * No-change rebuild for libgsl soname change.

 -- Matthias Klose <email address hidden>  Sun, 06 Aug 2017 00:16:58 +0000

Available diffs

• diff from 3.3.0-5 (in Debian) to 3.3.0-5build1 (336 bytes)

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 <email address hidden>  Fri, 29 Apr 2016 13:29:14 +0200

Available diffs

• diff from 3.3.0-4build1 (in Ubuntu) to 3.3.0-5 (1.3 KiB)

theseus (3.3.0-4build1) xenial; urgency=medium

  * Rebuild against new gsl SONAME change.

 -- Michael Terry <email address hidden>  Tue, 08 Dec 2015 09:17:24 -0500

Available diffs

• diff from 3.3.0-4 (in Debian) to 3.3.0-4build1 (330 bytes)

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 <email address hidden>  Wed, 25 Nov 2015 18:01:44 +0100

Available diffs

• diff from 3.3.0-3build1 (in Ubuntu) to 3.3.0-4 (1.4 KiB)

theseus (3.3.0-3build1) xenial; urgency=medium

  * Rebuild against new gsl. Update references to libgsl0-dev to libgsl-
    dev.

 -- Iain Lane <email address hidden>  Tue, 10 Nov 2015 15:08:27 +0000

Available diffs

• diff from 3.3.0-3 (in Debian) to 3.3.0-3build1 (518 bytes)

theseus (3.3.0-3) unstable; urgency=medium

  * Fix versioning which really
    Closes: #790515

 -- Andreas Tille <email address hidden>  Tue, 07 Jul 2015 09:03:03 +0200

Available diffs

• diff from 3.3.0-2 to 3.3.0-3 (481 bytes)

theseus (3.3.0-2) unstable; urgency=medium

  * Fix package split issue
    Closes: #790515

 -- Andreas Tille <email address hidden>  Wed, 01 Jul 2015 10:12:21 +0200

Available diffs

• diff from 3.3.0-1 to 3.3.0-2 (481 bytes)

theseus (3.3.0-1) unstable; urgency=medium

  * New upstream version
  * Add missing license statement
    Closes: #790311

 -- Andreas Tille <email address hidden>  Sun, 28 Jun 2015 15:04:59 +0200

Available diffs

• diff from 3.0.0-1 to 3.3.0-1 (20.6 MiB)
• diff from 3.1.1-1 to 3.3.0-1 (174.2 KiB)

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 <email address hidden>  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 <email address hidden>  Tue, 20 May 2014 15:08:38 +0200

Available diffs

• diff from 2.0.6-1 to 3.0.0-1 (244.5 KiB)

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 <email address hidden>  Wed, 26 Jun 2013 16:34:53 +0200

Available diffs

• diff from 1.6.2-2ubuntu1 (in Ubuntu) to 2.0.6-1 (79.2 KiB)

theseus (1.6.2-2ubuntu1) raring; urgency=low

  * Added missing math lib to link, fixing FTBFS.
 -- Daniel T Chen <email address hidden>   Mon, 15 Apr 2013 14:11:34 -0400

Available diffs

• diff from 1.6.2-2 (in Debian) to 1.6.2-2ubuntu1 (1.1 KiB)

theseus (1.6.2-2) unstable; urgency=low


  * debian/upstream: Added missing space, fixed Name
  * debian/patches: Two patches from Simon Ruderich
    <email address hidden> to enable hardening (thanks to Simon)
    Closes: #668120

 -- Andreas Tille <email address hidden>  Fri, 08 Jun 2012 08:45:38 +0200

Available diffs

• diff from 1.6.2-1 to 1.6.2-2 (1.7 KiB)

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 <email address hidden>  Sat, 24 Mar 2012 07:48:57 +0100

Available diffs

• diff from 1.6.1-1 (in Ubuntu) to 1.6.2-1 (155.2 KiB)

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.
 -- Ubuntu Archive Auto-Sync <email address hidden>   Sat,  30 Apr 2011 13:51:34 +0000

Available diffs

• diff from 1.5.5-1 to 1.6.1-1 (221.0 KiB)

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
 -- Ubuntu Archive Auto-Sync <email address hidden>   Thu,  25 Nov 2010 12:54:38 +0000

Available diffs

• diff from 1.4.3-2 to 1.5.5-1 (124.4 KiB)

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

Available diffs

• diff from 1.3.9-1ubuntu1 to 1.4.3-2 (38.4 KiB)

theseus (1.3.9-1ubuntu1) jaunty; urgency=low

  * 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. This fix will be available
    from Debian in release -2, at which point this Ubuntu merge can
    be dropped.
  * Ubuntu maintainer mangling.

Available diffs

• diff from 1.1.5-0ubuntu5 to 1.3.9-1ubuntu1 (138.9 KiB)

theseus (1.1.5-0ubuntu5) jaunty; urgency=low

  * Fix FTBFS on armel, lpia platforms using liblapack-dev in
    Build-Depends instead of liblapack3gf

 -- Morten Kjeldgaard <email address hidden>   Wed, 10 Dec 2008 16:52:55 +0100

Available diffs

• diff from 1.1.5-0ubuntu4 to 1.1.5-0ubuntu5 (508 bytes)

theseus (1.1.5-0ubuntu4) jaunty; urgency=low

  * FTBFS on armel, lpia platforms fixed by using liblapack3gf
    in Build-Depends instead of libatlas-base-dev.

 -- Morten Kjeldgaard <email address hidden>   Wed, 10 Dec 2008 14:46:54 +0100

Available diffs

• diff from 1.1.5-0ubuntu3 to 1.1.5-0ubuntu4 (567 bytes)

theseus (1.1.5-0ubuntu3) intrepid; urgency=low

  * gfortran transition for intrepid, atlas3-base -> libatlas3-base.

 -- Morten Kjeldgaard <email address hidden>   Thu, 04 Sep 2008 23:20:52 +0200

Available diffs

• diff from 1.1.5-0ubuntu2 to 1.1.5-0ubuntu3 (562 bytes)

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 <email address hidden>   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 <email address hidden>   Sun, 02 Dec 2007 15:53:15 +0100