Change log for libbpp-phyl package in Ubuntu

libbpp-phyl (2.4.1-9.1ubuntu3) noble; urgency=medium

  * No-change rebuild against libbpp-core4t64

 -- Steve Langasek <email address hidden>  Sun, 07 Apr 2024 07:28:24 +0000

Available diffs

• diff from 2.4.1-9.1ubuntu2 to 2.4.1-9.1ubuntu3 (322 bytes)

libbpp-phyl (2.4.1-9.1ubuntu2) noble; urgency=medium

  * No-change rebuild for CVE-2024-3094

 -- Steve Langasek <email address hidden>  Sun, 31 Mar 2024 18:51:43 +0000

Available diffs

• diff from 2.4.1-9.1ubuntu1 to 2.4.1-9.1ubuntu2 (331 bytes)

libbpp-phyl (2.4.1-9.1ubuntu1) noble; urgency=medium

  * Merge with Debian; remaining changes:
    - Build without LTO on s390x and arm64 as this causes misbehavior that
      breaks bppsuite.

Available diffs

• diff from 2.4.1-9ubuntu1 to 2.4.1-9.1ubuntu1 (124.0 KiB)

libbpp-phyl (2.4.1-9ubuntu1) noble; urgency=medium

  * Merge from Debian unstable. Remaining changes:
    - Build without LTO on s390x and arm64 as this causes misbehavior that
      breaks bppsuite.

Available diffs

• diff from 2.4.1-8ubuntu1 to 2.4.1-9ubuntu1 (6.2 KiB)

libbpp-phyl (2.4.1-8ubuntu1) lunar; urgency=low

  * Merge from Debian unstable. Remaining changes:
    - Build without LTO on s390x and arm64 as this causes misbehavior that
      breaks bppsuite.

Available diffs

• diff from 2.4.1-7ubuntu1 to 2.4.1-8ubuntu1 (6.6 KiB)

libbpp-phyl (2.4.1-7ubuntu1) kinetic; urgency=low

  * Merge from Debian unstable. Remaining changes:
    - Build without LTO on s390x and arm64 as this causes misbehavior that
      breaks bppsuite.

Available diffs

• diff from 2.4.1-6ubuntu1 to 2.4.1-7ubuntu1 (6.8 KiB)

libbpp-phyl (2.4.1-6ubuntu1) kinetic; urgency=medium

  * Build without LTO on s390x and arm64 as this causes misbehavior that
    breaks bppsuite.

 -- Steve Langasek <email address hidden>  Wed, 06 Jul 2022 15:44:53 +0000

Available diffs

• diff from 2.4.1-4 (in Debian) to 2.4.1-6ubuntu1 (5.5 KiB)
• diff from 2.4.1-6 (in Debian) to 2.4.1-6ubuntu1 (736 bytes)

libbpp-phyl (2.4.1-6) unstable; urgency=medium

  * Fix symbols again
    Closes: #997444

 -- Andreas Tille <email address hidden>  Mon, 01 Nov 2021 14:08:45 +0100

Available diffs

• diff from 2.4.1-5 to 2.4.1-6 (3.4 KiB)

libbpp-phyl (2.4.1-5) unstable; urgency=medium

  * Fix watchfile to detect new versions on github (routine-update)
  * Standards-Version: 4.6.0 (routine-update)
  * Update symbols to gcc 11
    Closes: #984089

 -- Andreas Tille <email address hidden>  Wed, 29 Sep 2021 20:23:09 +0200

libbpp-phyl (2.4.1-4) unstable; urgency=medium

  * Standards-Version: 4.5.0 (routine-update)
  * debhelper-compat 13 (routine-update)
  * Add salsa-ci file (routine-update)
  * Rules-Requires-Root: no (routine-update)
  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
    Repository-Browse.
  * Refer to specific version of license GPL-2+.
  * Fix day-of-week for changelog entry 2.0.3-1.
  * Update symbols for gcc-10
    Closes: #957425

 -- Andreas Tille <email address hidden>  Thu, 23 Jul 2020 11:44:02 +0200

Available diffs

• diff from 2.4.1-3build1 (in Ubuntu) to 2.4.1-4 (16.7 KiB)

libbpp-phyl (2.4.1-3build1) focal; urgency=medium

  * No-change rebuild for libgcc-s1 package name change.

 -- Matthias Klose <email address hidden>  Mon, 23 Mar 2020 07:17:50 +0100

Available diffs

• diff from 2.4.1-3 (in Debian) to 2.4.1-3build1 (326 bytes)

libbpp-phyl (2.4.1-3) unstable; urgency=medium

  [ Julien Dutheil ]
  * Remove test that causes random failures

  [ Andreas Tille ]
  * Adapt symbols to new gcc version
    Closes: #925732
  * debhelper-compat 12
  * Standards-Version: 4.4.0

 -- Andreas Tille <email address hidden>  Tue, 20 Aug 2019 18:13:57 +0200

Available diffs

• diff from 2.4.1-2 to 2.4.1-3 (13.0 KiB)

libbpp-phyl (2.4.1-2) unstable; urgency=medium

  [ Jelmer Vernooij ]
  * Use secure copyright file specification URI.
  * Trim trailing whitespace.

  [ Michael R. Crusoe ]
  * libbpp-phyl-dev: Multi-Arch: same & add missing ${devlibs:Depends}
  * Remove trailing whitespace in debian/copyright
  * Standards-Version: 4.3.0

  [ Andreas Tille ]
  * Adapt symbols to new gcc version
    Closes: #923457
  * More sensible way to provide symbols amd64 only

 -- Andreas Tille <email address hidden>  Fri, 01 Mar 2019 15:52:37 +0100

Available diffs

• diff from 2.4.1-1 to 2.4.1-2 (125.4 KiB)

libbpp-phyl (2.4.1-1) unstable; urgency=medium

  [ Julien Dutheil ]
  * New upstream update.
    Closes: #906478 

  [ Andreas Tille ]
  * Standards-Version: 4.2.0

 -- Julien Dutheil <email address hidden>  Sun, 19 Aug 2018 21:36:23 +0200

Available diffs

• diff from 2.4.0-2 to 2.4.1-1 (126.2 KiB)

libbpp-phyl (2.4.0-2) unstable; urgency=medium

  [ Julien Dutheil ]
  * Increases likelihood test tolerance.

  [ Andreas Tille ]
  * Standards-Version: 4.1.4

 -- Julien Dutheil <email address hidden>  Mon, 30 Apr 2018 16:58:46 +0200

Available diffs

• diff from 2.4.0-1 to 2.4.0-2 (1.6 KiB)

libbpp-phyl (2.4.0-1) unstable; urgency=medium

  [ Julien Dutheil ]
  * New upstream update.
  * Reduced execution time of test_likelihood_nh
    Closes: #890136
  * Added symbol list (only for amd64)

  [ Andreas Tille ]
  * Versioned Build-Depends: d-shlibs (>= 0.82)
  * d/rules: Drop unneeded override for d-shlibmove
  * Provide full license text of CeCILL license
  * Point Vcs fields to salsa.debian.org

 -- Julien Dutheil <email address hidden>  Fri, 06 Apr 2018 07:53:20 +0200

Available diffs

• diff from 2.3.1-10 to 2.4.0-1 (219.8 KiB)
• diff from 2.3.2-2build1 (in Ubuntu) to 2.4.0-1 (117.7 KiB)

libbpp-phyl (2.3.2-2build1) bionic; urgency=medium

  * No-change rebuild against libbpp-core4

 -- Steve Langasek <email address hidden>  Mon, 09 Apr 2018 07:59:42 +0000

Available diffs

• diff from 2.3.2-2 (in Debian) to 2.3.2-2build1 (534 bytes)

libbpp-phyl (2.3.2-2) unstable; urgency=medium

  * Fixed covariant return type on 32bits arch.
    Closes: #889953

 -- Julien Dutheil <email address hidden>  Fri, 09 Feb 2018 09:10:11 +0200

Available diffs

• diff from 2.3.2-1 to 2.3.2-2 (772 bytes)

libbpp-phyl (2.3.2-1) unstable; urgency=medium

  [ Julien Dutheil ]
  * Standards-Version: 4.1.2

  [ Andreas Tille ]
  * cme fix dpkg-control
  * debhelper 11

 -- Julien Dutheil <email address hidden>  Mon, 05 Feb 2018 20:59:41 +0200

libbpp-phyl (2.3.1-10) unstable; urgency=medium

  [ Julien Dutheil ]
  * Does not override debian cxx flags anymore.

  [ Andreas Tille ]
  * Rebuild with gcc-7
    Closes: #871085
  * Standards-Version: 4.0.1
  * Fix d-shlibs override

 -- Andreas Tille <email address hidden>  Wed, 23 Aug 2017 23:32:26 +0200

Available diffs

• diff from 2.3.1-9 to 2.3.1-10 (3.0 KiB)

libbpp-phyl (2.3.1-9) unstable; urgency=medium

  * Further increased time out limit for unit tests.
    Closes: 866365

 -- Julien Dutheil <email address hidden>  Mon, 17 Jul 2017 09:24:23 +0200

Available diffs

• diff from 2.3.1-8 to 2.3.1-9 (559 bytes)

libbpp-phyl (2.3.1-8) unstable; urgency=medium

  * another try to have test_likelihood_clock pass on mips architecture.

 -- Julien Dutheil <email address hidden>  Sun, 16 Jul 2017 10:43:18 +0200

Available diffs

• diff from 2.3.1-7 to 2.3.1-8 (1.4 KiB)

libbpp-phyl (2.3.1-7) unstable; urgency=medium

  * Some tests redesign.
    Should hopefully make test_mapping more stable, and have
    test_likelihood_clock pass on mips architecture

 -- Julien Dutheil <email address hidden>  Sat, 15 Jul 2017 22:48:50 +0200

Available diffs

• diff from 2.3.1-6 to 2.3.1-7 (3.2 KiB)

libbpp-phyl (2.3.1-6) unstable; urgency=medium

  [ Julien Dutheil ]
  * remove some deprecation warnings which might lead to timeouts in tests

  [ Andreas Tille ]
  * Remove postinst, postrm and prerm

 -- Andreas Tille <email address hidden>  Fri, 14 Jul 2017 14:20:59 +0200

Available diffs

• diff from 2.3.1-5 to 2.3.1-6 (2.7 KiB)

libbpp-phyl (2.3.1-5) unstable; urgency=medium

  * Fix build time issues for remaining architectures
    Closes: #865552

 -- Andreas Tille <email address hidden>  Tue, 27 Jun 2017 11:16:14 +0200

Available diffs

• diff from 2.3.1-4 to 2.3.1-5 (1.2 KiB)

libbpp-phyl (2.3.1-4) unstable; urgency=medium

  * Relax timeout for tests.
    Dealswith: #865552
  * d-shlibs (>= 0.80) contains needed override

 -- Andreas Tille <email address hidden>  Mon, 26 Jun 2017 12:39:58 +0200

Available diffs

• diff from 2.2.0-1 to 2.3.1-4 (203.8 KiB)
• diff from 2.3.1-3 to 2.3.1-4 (1015 bytes)

libbpp-phyl (2.3.1-3) unstable; urgency=medium

  * cmake files belong to /usr/lib/$(DEB_HOST_MULTIARCH)
  * debhelper 10
  * Standards-Version: 4.0.0 (no changes needed)

 -- Andreas Tille <email address hidden>  Fri, 23 Jun 2017 09:10:34 +0200

Available diffs

• diff from 2.3.1-2 to 2.3.1-3 (769 bytes)

libbpp-phyl (2.3.1-2) unstable; urgency=medium

  * Make sure cmake files will be installed also on i386

 -- Andreas Tille <email address hidden>  Thu, 22 Jun 2017 08:03:24 +0200

Available diffs

• diff from 2.3.1-1 to 2.3.1-2 (476 bytes)

libbpp-phyl (2.3.1-1) unstable; urgency=medium

  * New upstream version
  * d/watch: point to github

 -- Andreas Tille <email address hidden>  Tue, 13 Jun 2017 16:39:48 +0200

libbpp-phyl (2.2.0-1) unstable; urgency=medium

  * New upstream version
  * Moved packaging to Git
  * Better description
  * Team maintenance in Debian Med team
  * cme fix dpkg-control
  * Source package section: science
  * Add watch file
  * debhelper 9
  * DEP5
  * short dh rules file using d-shlibs
  * Library transition
    Closes: #791094

 -- Andreas Tille <email address hidden>  Thu, 21 Apr 2016 14:16:41 +0200

Available diffs

• diff from 2.1.0-1ubuntu3 (in Ubuntu) to 2.2.0-1 (198.9 KiB)

libbpp-phyl (2.1.0-1ubuntu3) wily; urgency=medium

  * And again, drop hardcoded dep.

 -- Iain Lane <email address hidden>  Tue, 11 Aug 2015 13:19:39 +0100

Available diffs

• diff from 2.1.0-1 (in Debian) to 2.1.0-1ubuntu3 (1021 bytes)
• diff from 2.1.0-1ubuntu2 to 2.1.0-1ubuntu3 (489 bytes)

libbpp-phyl (2.1.0-1ubuntu2) wily; urgency=medium

  * No-change rebuild against new libbpp-seq

 -- Iain Lane <email address hidden>  Tue, 11 Aug 2015 12:27:42 +0100

Available diffs

• diff from 2.1.0-1ubuntu1 to 2.1.0-1ubuntu2 (340 bytes)

libbpp-phyl (2.1.0-1ubuntu1) wily; urgency=medium

  * Rename library packages for g++5 ABI transition.

 -- Steve Langasek <email address hidden>  Tue, 04 Aug 2015 04:41:54 +0000

Available diffs

• diff from 2.1.0-1 (in Debian) to 2.1.0-1ubuntu1 (912 bytes)

libbpp-phyl (2.1.0-1) unstable; urgency=low


  * New RateDistribution classes
  * New models for protein sequences (COaLA)
  * Support for gaps in parsimony score
  * Improved and extended support for BppO
  * Several bugs fixed and warnings removed

 -- Julien Dutheil <email address hidden>  Thu, 07 Mar 2013 15:58:00 +0100

Available diffs

• diff from 2.0.3-1 to 2.1.0-1 (511.6 KiB)

libbpp-phyl (2.0.3-1) unstable; urgency=low


  * Reorganized model hierarchy
  * New pairwise models
  * Several bugs fixed

 -- Julien Dutheil <email address hidden>  Thu, 09 Feb 2013 16:00:00 +0100

Available diffs

• diff from 2.0.2-1 (in Ubuntu) to 2.0.3-1 (148.9 KiB)

libbpp-phyl (2.0.2-1) unstable; urgency=low

  * RFP: Bio++ -- The Bio++ bioinformatics libraries. (Closes: #616373).
  * Packages are now non-native.
  * Exact substitution mapping with detailled counts.
  * Backup system for ML estimation.