Change log for bioperl package in Ubuntu

bioperl (1.7.8-1) unstable; urgency=medium

  * Team Upload.
  * New upstream version 1.7.8
  * Remove d/p/FTlineParsingHickups.patch: merged upstream
  * Bump debhelper-compat version to 13
  * Declare compliance with policy 4.5.1
  * Add d/salsa-ci.yml

 -- Nilesh Patra <email address hidden>  Sun, 15 Aug 2021 18:26:03 +0530

Available diffs

• diff from 1.7.7-2 to 1.7.8-1 (34.4 KiB)

bioperl (1.7.7-2) unstable; urgency=medium

  * Prepared patch to parse current feature table layout
  * d/control: updated standard to 4.5, added R-R-R: no

 -- Steffen Moeller <email address hidden>  Wed, 28 Oct 2020 18:49:40 +0100

Available diffs

• diff from 1.7.7-1 to 1.7.7-2 (1.2 KiB)

bioperl (1.7.7-1) unstable; urgency=medium

  * Team upload.
  * New upstream release.

 -- Michael R. Crusoe <email address hidden>  Sat, 14 Dec 2019 22:48:17 +0100

Available diffs

• diff from 1.7.6-3 to 1.7.7-1 (33.2 KiB)

bioperl (1.7.6-3) unstable; urgency=medium

  * Team upload.
  * Really fix the breaks+replaces for libbio-perl-run-perl (Closes: #921495)

 -- Michael R. Crusoe <email address hidden>  Thu, 28 Nov 2019 13:06:59 +0100

Available diffs

• diff from 1.7.2-3 to 1.7.6-3 (5.1 MiB)
• diff from 1.7.6-2 to 1.7.6-3 (518 bytes)

bioperl (1.7.6-2) unstable; urgency=medium

  * Team upload.
  * Add breaks: roary <= 3.12.0+dfsg-2

 -- Michael R. Crusoe <email address hidden>  Wed, 27 Nov 2019 11:48:16 +0100

Available diffs

• diff from 1.7.6-1 to 1.7.6-2 (471 bytes)

bioperl (1.7.6-1) unstable; urgency=medium

  * Team upload.
  * Fix autopkgtests:
      Don't run the `use.t` autopkgtest, there is no longer a Bio::Perl module
      scripts/ → bin/
      No Build.PL anymore, skip it
  * Add missing colon in closes line.
  * Set fields Upstream-Name, Upstream-Contact in debian/copyright.
  * Set upstream metadata fields: Repository-Browse.
  * Remove obsolete fields Name, Contact from debian/upstream/metadata.
  * New upstream release.
  * No longer conflicts with libbio-perl-run-perl (Closes: #921495)
  * Fixed some spelling typos

 -- Michael R. Crusoe <email address hidden>  Tue, 26 Nov 2019 11:22:39 +0100

Available diffs

• diff from 1.7.5-1 to 1.7.6-1 (40.2 KiB)

bioperl (1.7.5-1) unstable; urgency=medium

  * New upstream version
  * Packaged with routine-update script
  * debhelper-compat 12
  * Standards-Version: 4.4.0

 -- Steffen Moeller <email address hidden>  Sat, 27 Jul 2019 17:55:00 +0200

Available diffs

• diff from 1.7.4-1 to 1.7.5-1 (113.4 KiB)

bioperl (1.7.4-1) unstable; urgency=medium

  * New upstream version
  * Drop broken uversionmangle from watch file
  * debhelper 12
  * Standards-Version: 4.3.0
  * Build-Depends: libyaml-perl, libtest-requiresinternet-perl
  * Drop manual renaming and permission fixes which are not needed
    any more
  * More fixes to Perl path in examples

 -- Andreas Tille <email address hidden>  Tue, 05 Feb 2019 22:17:53 +0100

Available diffs

• diff from 1.7.2-3 to 1.7.4-1 (5.1 MiB)

bioperl (1.7.2-3) unstable; urgency=medium

  * debhelper 11
  * Point Vcs fields to salsa.debian.org
  * Standards-Version: 4.2.1
  * Remove trailing whitespace in debian/changelog
  * Remove trailing whitespace in debian/copyright
  * Remove trailing whitespace in debian/rules
  * Fix Perl interpreter path
  * Fix URL for source download

 -- Andreas Tille <email address hidden>  Sun, 28 Oct 2018 00:46:56 +0200

Available diffs

• diff from 1.7.2-2 to 1.7.2-3 (3.0 KiB)

bioperl (1.7.2-2) unstable; urgency=medium

  * Team upload

  [ gregor herrmann ]
  * Fix autopkgtests. The smoke tests need a `perl Build.PL' beforehand.
    And we need some additional files for some tests. (Closes: #871727)
  * debian/control: move libmodule-build-perl to Build-Depends from Build-
    Depends-Indep. It is needed during clean.

  [ Andreas Tille ]
  * Standards-Version: 4.1.2
  * Secure URI in watch file

 -- gregor herrmann <email address hidden>  Wed, 13 Dec 2017 21:59:15 +0100

Available diffs

• diff from 1.7.1-3 to 1.7.2-2 (194.8 KiB)
• diff from 1.7.2-1 to 1.7.2-2 (1.2 KiB)

bioperl (1.7.2-1) unstable; urgency=medium

  * New upstream version
  * Standards-Version: 4.1.1

 -- Andreas Tille <email address hidden>  Sun, 03 Dec 2017 18:55:57 +0100

bioperl (1.7.1-3) unstable; urgency=medium

  * Team upload

  [ Carnë Draug ]
  * Declare missing dependency on libtest-most-perl used by
    Bio::Root::Test

  [ Andreas Tille ]
  * Build-Depends: rename
    Closes: #873745
  * Standards-Version: 4.1.0 (no changes needed)

 -- Carnë Draug <email address hidden>  Wed, 30 Aug 2017 14:56:14 +0100

Available diffs

• diff from 1.7.1-2 to 1.7.1-3 (887 bytes)

bioperl (1.7.1-2) unstable; urgency=medium

  [ gregor herrmann ]
  * Add debian/tests/pkg-perl/use-name to fix an autopkgtest failure
  * Add t/Perl.t and t/Species.t to debian/tests/pkg-perl/smoke-skip

 -- Andreas Tille <email address hidden>  Sun, 15 Jan 2017 08:50:21 +0100

Available diffs

• diff from 1.6.924-5 to 1.7.1-2 (393.6 KiB)
• diff from 1.7.1-1 to 1.7.1-2 (430 bytes)

bioperl (1.7.1-1) unstable; urgency=medium

  [ Charles Plessy ]
  * New upstream release.
    Closes: #846579
  * debian/patches deleted (applied upstream).
  * debian/docs: correct name of README file.
  * debian/control: Use secure VCS browser URL.

  [ Andreas Tille ]
  * d/watch: uversionmangle to get proper version number
  * debhelper 10

 -- Andreas Tille <email address hidden>  Mon, 05 Dec 2016 22:05:08 +0100

bioperl (1.6.924-5) unstable; urgency=medium

  * Testsuite: autopkgtest-pkg-perl
  * Move packaging from SVN to Git

 -- Andreas Tille <email address hidden>  Wed, 29 Jun 2016 09:20:14 +0200

Available diffs

• diff from 1.6.924-4 to 1.6.924-5 (692 bytes)

bioperl (1.6.924-4) unstable; urgency=medium

  * cme fix dpkg-control (Needed several manual postprocessing since cme
    has the habit to move comments to the end of a section)
  * Fix FTBFS with Perl 5.24 by applying upstream patch
    Closes: #825429
  * Remove unused paragraph in d/copyright

 -- Andreas Tille <email address hidden>  Sun, 05 Jun 2016 08:50:03 +0200

Available diffs

• diff from 1.6.924-3 to 1.6.924-4 (3.2 KiB)

bioperl (1.6.924-3) unstable; urgency=medium

  * Fix FTBFS with perl 5.22
    Closes: #796259
  * Standards-Version: 3.9.6

 -- Andreas Tille <email address hidden>  Thu, 20 Aug 2015 23:11:32 +0200

Available diffs

• diff from 1.6.924-2 to 1.6.924-3 (653 bytes)

bioperl (1.6.924-2) unstable; urgency=medium

  * d/control: add perl-modules for perl 5.22 transition
               (Closes: #790305). 

 -- Olivier Sallou <email address hidden>  Mon, 29 Jun 2015 09:05:22 +0200

Available diffs

• diff from 1.6.924-1 to 1.6.924-2 (533 bytes)

bioperl (1.6.924-1) unstable; urgency=medium


  * New upstream release.

 -- Charles Plessy <email address hidden>  Sun, 13 Jul 2014 19:16:01 +0900

Available diffs

• diff from 1.6.923-1 to 1.6.924-1 (300.5 KiB)

bioperl (1.6.923-1) unstable; urgency=medium


  * New upstream release.
  * Does not need non-free libmath-random-perl anymore.
  * Build-depend on libmodule-build-perl (>= 0.420000).  Despite Lintian's
    warning that it is useless, the package does not build without.
  * Conforms to Policy version 3.9.5.

 -- Charles Plessy <email address hidden>  Sat, 18 Jan 2014 11:41:11 +0900

Available diffs

• diff from 1.6.922-1 to 1.6.923-1 (64.9 KiB)

bioperl (1.6.922-1) unstable; urgency=low


  * New upstream release.
  * Replaces and Breaks grinder (<< 0.5.3-3~) because of overlaping contents.
    Closes: #722910
  * Stop Replacing and Breaking bioperl ( << 1.6.9 ): not needed anymore. 

 -- Charles Plessy <email address hidden>  Sun, 22 Sep 2013 13:39:48 +0900

Available diffs

• diff from 1.6.901-4 to 1.6.922-1 (1.3 MiB)

bioperl (1.6.901-4) unstable; urgency=low


  * debian/upstream: Add additional citation data
  [ Olivier Sallou ]
  * add missing dependency
  * Switch to standards 3.9.4

 -- Andreas Tille <email address hidden>  Tue, 08 May 2012 23:06:09 +0200

Available diffs

• diff from 1.6.901-3 to 1.6.901-4 (1.5 KiB)

bioperl (1.6.901-3) unstable; urgency=low


  * Team upload.
    [ Olivier Sallou ]
    + add patch fix_berkeleydb3_temp_file_creation (Closes: #661793).
      Fixed upstream for next release. 
    * debian/control: update Standards version
    * debian/copyright: update Format to latest officiel URL v1.0
    * debian/patches/fix_examples_perl_location: fix wrong perl location
    * debian/rules: fix file access rights in dh_install

 -- Olivier Sallou <email address hidden>  Fri, 02 Mar 2012 11:10:36 +0100

Available diffs

• diff from 1.6.901-2 (in Ubuntu) to 1.6.901-3 (5.8 KiB)

bioperl (1.6.901-2) unstable; urgency=low

  [ Luca Capello ]
  * debian/control:
    + add Recommends: to some libraries already in libbio-perl-perl's
      for binaries showing help output (Closes: #650412).
  * debian/README.Debian:
    + new file with a more detailed explanation about the above.

  [ Andreas Tille ]
  * debian/source/format: 3.0 (quilt)
  * Added myself to Uploaders
 -- Ubuntu Archive Auto-Sync <email address hidden>   Mon,  26 Dec 2011 17:47:33 +0000

Available diffs

• diff from 1.6.901-1 to 1.6.901-2 (4.7 KiB)

bioperl (1.6.901-1) unstable; urgency=low

  * New upstream release.
  * Point debian/watch to search.cpan.org.
  * Build using dh and overrides:
    - Use Debhelper 8 (debian/rules, debian/control).
    - Simplified debian/rules.
  * Split into libbio-perl-perl, as discussed with the Debian Perl team.
    (debian/control, debian/bioperl.install, debian libbio-perl-perl.install)
  * debian/control:
    - Incremented Standards-Version to reflect conformance with Policy 3.9.2.
      No other changes needed.
    - Vcs-Browser URL made redirectable to viewvc.
    - Removed useless ‘svn’ in the Vcs-Svn URL.
 -- Ubuntu Archive Auto-Sync <email address hidden>   Fri,  17 Jun 2011 22:56:18 +0000

Available diffs

• diff from 1.6.1-2 to 1.6.901-1 (1.9 MiB)

bioperl (1.6.1-2) unstable; urgency=low

  * Removed bibliographic information from the long description
    (debian/control).
  * Incremented Standards-Version to reflect conformance with Policy 3.8.4
    (debian/control, no changes needed).
  * Build-depends on libxml-sax-expatxs-perl to avoid downloading DTDs during
    the tests and therefore fail when network is not available
    (debian/control, Closes: #562442).
  * Depend on the ${misc:Depends} substvar (debian/control).
 -- Ubuntu Archive Auto-Sync <email address hidden>   Tue,  18 May 2010 15:24:49 +0100

Available diffs

• diff from 1.6.1-1ubuntu1 to 1.6.1-2 (2.6 KiB)

bioperl (1.6.1-1ubuntu1) lucid; urgency=low

  * Merge from Debian testing, remaining changes:
    - disable tests, they produce a FTBFS trying to access the network
      during run.

Available diffs

• diff from 1.6.0-2ubuntu1 to 1.6.1-1ubuntu1 (1.9 MiB)

bioperl (1.6.0-2ubuntu1) karmic; urgency=low

  * disable tests, they produce a FTBFS trying to access the network
    during run.
    - Debian report: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=533976
    - Upstream report: http://bugzilla.open-bio.org/show_bug.cgi?id=2861

 -- Andreas Moog <email address hidden>   Tue, 04 Aug 2009 00:13:02 +0200

Available diffs

• diff from 1.6.0-2 to 1.6.0-2ubuntu1 (788 bytes)

bioperl (1.6.0-2) unstable; urgency=low

  * Removed patch system (not used):
    - removed instuctions in debian/rules;
    - removed quilt from Build-Depends in debian/control.
  * Re-enabled tests:
    - uncommented test command in debian/rules;
    - uncommented previously missing build-dependencies in debian/control.
    - Re-enabled tests and uncommented build-dependencies accordingly.
  * Removed libmodule-build-perl and libtest-harness-perl from
    Build-Depends-Indep (provided by perl-modules).
  * Better cleaning of empty directories using find -type d -empty -delete
    instead of rmdir in debian/rules (LP: #324001).

Available diffs

• diff from 1.5.2.102-3 to 1.6.0-2 (2.5 MiB)

bioperl (1.5.2.102-3) unstable; urgency=low

  * debian/control:
    - Removed MIA Matt Hope (dopey) from the Uploaders field.
      Thank you for your work, Matt. I hope you are doing well.
    - Downgraded some recommended package to the 'Suggests' priority,
      according to the following discussion on Upstream's mail list.
      http://bioperl.org/pipermail/bioperl-l/2008-March/027379.html
      (Closes: #448890)
  * debian/copyright converted to machine-readable format.

Available diffs

• diff from 1.5.2.102-1ubuntu1 to 1.5.2.102-3 (7.7 KiB)

bioperl (1.5.2.102-1ubuntu1) hardy; urgency=low

  * debian/control:
    + Add libio-string-perl to Build-Depends-Indep.
    + Modify Maintainer value to match DebianMaintainerField spec.

 -- Michael Bienia <email address hidden>   Tue, 29 Jan 2008 20:27:50 +0100

bioperl (1.5.2.102-1) unstable; urgency=low

  * Developer release.
  * Upgraded source package to debhelper 5 and standards-version 3.7.2.
  * Added libmodule-build-perl and libtest-harness-perl to
    build-depends-indep.
  * Disabled automatic CRAN download.
  * Using quilt instead of .diff.gz to manage modifications.
  * Updated Recommends list for the binary package.
  * Moved the "production-quality" scripts to /usr/bin/.
  * New maintainer: Debian-Med packaging team mailing list.
  * New uploaders: Charles Plessy and Steffen Moeller.
  * Updated Depends, Recommends and Suggests.
  * Imported in Debian-Med's SVN repository on Alioth.
  * Executing the regression tests during package building.
  * Moved the Homepage: field out from the package's description.
  * Updated watch file.

 -- Ubuntu Archive Auto-Sync <email address hidden>   Sat,  03 Nov 2007 13:07:50 +0000

bioperl (1.4-1) unstable; urgency=low


  * New upstream release
  * Examples and working code are installed by default to usr/bin,
    this has been moved to usr/share/doc/bioperl/bin

 -- Matt Hope <email address hidden>  Sun, 18 Apr 2004 14:24:11 +1000

bioperl (1.2.1-2) unstable; urgency=low


  * Updated dependancies to libgd-gd2-perl
    (Closes: Bug#192210)
  * Same maintainer, different email address

 -- Matt Hope <email address hidden>  Mon, 30 Jun 2003 23:40:59 +1000