Change log for bioperl-run package in Ubuntu

bioperl-run (1.7.3-9) unstable; urgency=medium

  [ Andreas Tille ]
  * Fix test data in BEDtools test
  * Fix upstream source download name in watch file
  * Standards-Version: 4.6.2 (routine-update)
  * Update lintian override info format in d/bioperl-run.lintian-overrides on
    line 2-6.

  [ Étienne Mollier ]
  * d/control: depend on libsoap-lite-perl.
  * d/t/p/smoke-skip: skip test only suitable for build time.

 -- Étienne Mollier <email address hidden>  Sun, 22 Jan 2023 12:26:27 +0100

Available diffs

• diff from 1.7.3-8 to 1.7.3-9 (2.0 KiB)

bioperl-run (1.7.3-8) unstable; urgency=medium

  * Replace skip_tests_for_muscle.patch by adjust-muscle-test.patch.
    Integration of newer muscle version in debian changed the code path in
    the way the test may be skipped, breaking autopkgtest of bioperl-run.
  * Move libmodule-build-perl from Build-Depends-Indep to Build-Depends.

 -- Étienne Mollier <email address hidden>  Thu, 10 Feb 2022 20:44:28 +0100

Available diffs

• diff from 1.7.3-7 to 1.7.3-8 (1.9 KiB)

bioperl-run (1.7.3-7) unstable; urgency=medium

  * d/watch: fix broken link to github and adjust version mangling to fit
    upstream's tagging convention (tag "release-x-y-z" for version "x.y.z")
  * adjust lintian override on bp_bioperl_application_installer.pl file
    extension, which is not provided anymore
  * add fix-whatis-entries.patch; fixes lintian warnings on bad-whatis-entry
    by providing a convenient description in the NAME field where needed
  * add unscramble-erpin.patch; fixes a kind of typo in ERPIN.pm documentation,
    flagged by lintian warning national-encoding
  * add fix-pod-conversion.patch; address the lintian warning
    pod-conversion-message affecting Bio::DB::SoapEUtilities::Result.
  * d/control: add myself to uploaders
  * Standards-Version: 4.6.0 (routine-update)

 -- Étienne Mollier <email address hidden>  Tue, 14 Sep 2021 18:52:51 +0200

Available diffs

• diff from 1.7.3-6 to 1.7.3-7 (2.8 KiB)

bioperl-run (1.7.3-6) unstable; urgency=medium

  * Team upload.
  * d/control: restrict build-dependencies to their supported architectures.
  * added skip-test-for-kalign.patch

 -- Étienne Mollier <email address hidden>  Wed, 06 Jan 2021 22:38:23 +0100

Available diffs

• diff from 1.7.3-5 to 1.7.3-6 (1.2 KiB)

bioperl-run (1.7.3-5) unstable; urgency=medium

  * Team upload.

  [ Michael R. Crusoe ]
  * Add build-dep on libfile-sort-perl as that has arrived in Debian
  * debian/upstream/metadata: Add Repository & Repository-Browse

  [ Pranav Ballaney ]
  * Disable tests for RemoteBlast
  * Disable tests for RemoteBlast_rpsblast
  * Extract BEDTools version properly

  [ Andreas Tille ]
  * Depends: libfile-sort-perl
    Closes: #974168
  * Standards-Version: 4.5.1 (routine-update)
  * debhelper-compat 13 (routine-update)
  * Remove trailing whitespace in debian/control (routine-update)

  [ Étienne Mollier ]
  * Add get-overlap.patch to map to the proper "getOverlap" wrapper.
  * Add build time test dependencies to get BEDtools test data sets.
  * Add alternate-data.patch to use a dataset available in the Debian
    archive during build time testings.
  * Suppress retries when attempting to access remote Blast resources,
    this prevents hogging autopkgtest runners ten more minutes.

 -- Étienne Mollier <email address hidden>  Thu, 03 Dec 2020 21:57:37 +0100

Available diffs

• diff from 1.7.3-4 to 1.7.3-5 (4.8 KiB)

bioperl-run (1.7.3-4) unstable; urgency=medium

  [ Michael R. Crusoe ]
  * Team upload.
  * Fix the autopkgtests
  * Set 'Bio::Factory::EMBOSS' as the main module name for the purpose of
    the use.t autopkgtest
  * fix hyphympi autopkgtests
  * libipc-run-perl is needed for Bio::Tools::Run::BEDTools
  * drawgram is pary of the phylip package

  [ Pranav Ballaney ]
  * Change kalign command string to input via stdin It fails to take input
    via the -in flag during testing
  * Revert changes made outside of debian/
  * Update quilt version
  * Kalign takes input via a pipe
  * Extract Kalign version properly (Closes: #954511)

  [ Andreas Tille ]
  * Standards-Version: 4.5.0 (routine-update)
  * Add salsa-ci file (routine-update)
  * Rules-Requires-Root: no (routine-update)
  * Wrap long lines in changelog entries: 1.7.2-1.
  * Set upstream metadata fields: Bug-Submit.

 -- Pranav Ballaney <email address hidden>  Tue, 31 Mar 2020 01:13:25 +0530

Available diffs

• diff from 1.7.3-3 to 1.7.3-4 (3.7 KiB)

bioperl-run (1.7.3-3) unstable; urgency=medium

  * Team upload.
  * Depends: libbio-tools-run-alignment-clustalw-perl (Closes: #948323)
  * Depends: libbio-featureio-perl

 -- Michael R. Crusoe <email address hidden>  Tue, 07 Jan 2020 12:07:09 +0100

Available diffs

• diff from 1.7.3-1 to 1.7.3-3 (1.9 KiB)
• diff from 1.7.3-2 to 1.7.3-3 (473 bytes)

bioperl-run (1.7.3-2) unstable; urgency=medium

  * Depends: libbio-tools-run-alignment-clustalw
  * Build-Depends / Recommends: s/blast2/ncbi-blast+-legacy/
    Closes: #948082
  * debhelper-compat 12
  * Standards-Version: 4.4.1
  * Remove trailing whitespace in debian/changelog
  * Remove trailing whitespace in debian/copyright
  * Set upstream metadata fields: Bug-Database.

 -- Andreas Tille <email address hidden>  Sat, 04 Jan 2020 17:49:32 +0100

Available diffs

• diff from 1.7.3-1 to 1.7.3-2 (1.8 KiB)

bioperl-run (1.7.3-1) unstable; urgency=medium

  * New upstream version
  * debhelper 12
  * Standards-Version: 4.3.0
  * Drop dependencies: bowtie, bwa, maq, t-coffee, gmap, paml
    Thanks for the hint to Carnë Draug <email address hidden>)
  * Versioned (Build-)Depends: bioperl (>= 1.7.4)

 -- Andreas Tille <email address hidden>  Mon, 11 Feb 2019 22:14:53 +0100

Available diffs

• diff from 1.7.2-4 to 1.7.3-1 (1.2 MiB)

bioperl-run (1.7.2-4) unstable; urgency=medium

  * (Build-)Depends: ncoils
  * do not run tests parallel to get sensibly sorted output
  * Allow MPI oversubscription (as in phyml build since phyml caused
    problems inside build time tests)
    This is also not reliable - skip phyml test at all
    Closes: #906337
  * debhelper 11
  * Point Vcs fields to salsa.debian.org
  * Standards-Version: 4.2.1
  * Fix Homepage
  * Lintian-override for script-with-language-extension

 -- Andreas Tille <email address hidden>  Fri, 14 Sep 2018 20:10:08 +0200

Available diffs

• diff from 1.7.2-3 to 1.7.2-4 (3.8 KiB)

bioperl-run (1.7.2-3) unstable; urgency=medium

  * Drop adjust_bowtie_tests.patch, Closes: #887578
  * Bump Standards-Version to 4.1.3 (no changes needed)

 -- Alexandre Mestiashvili <email address hidden>  Fri, 26 Jan 2018 10:43:45 +0100

Available diffs

• diff from 1.7.1-3 to 1.7.2-3 (65.2 KiB)
• diff from 1.7.2-2 to 1.7.2-3 (584 bytes)

bioperl-run (1.7.2-2) unstable; urgency=medium

  * Team upload
  * Add adjust_bowtie_tests.patch fixing failing tests for Bowtie
    Closes: #880347
  * Bump Standards-Version to 4.1.2, apply cme fix dpkg

 -- Alexandre Mestiashvili <email address hidden>  Thu, 07 Dec 2017 18:19:04 +0100

Available diffs

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

bioperl-run (1.7.2-1) unstable; urgency=medium

  * New upstream version
  * Convert packaging from SVN to Git
  * For some reason Ensembl.t test is executed in autopkgtest run even
    if it should be skipped due to missing preconditions
    (http://search.cpan.org/~cjfields/Bio-EUtilities-1.72/lib/Bio/DB/EUtilities.pm)
    The test will now be fully removed to make sure it is skipped.
  * Standards-Version: 4.1.0 (no changes needed)
  * Do not try to run bowtie tests with wrong bowtie call
    Closes: #868073

 -- Andreas Tille <email address hidden>  Wed, 20 Sep 2017 14:29:45 +0200

bioperl-run (1.7.1-3) unstable; urgency=medium

  * s/Conflicts/Breaks/
    Closes: #850029

 -- Andreas Tille <email address hidden>  Fri, 13 Jan 2017 08:25:26 +0100

Available diffs

• diff from 1.7.1-1 to 1.7.1-3 (641 bytes)
• diff from 1.7.1-2 to 1.7.1-3 (523 bytes)

bioperl-run (1.7.1-2) unstable; urgency=medium

  * Conflicts: libbio-perl-perl (<< 1.7.1-1)
    Closes: #850029

 -- Andreas Tille <email address hidden>  Tue, 03 Jan 2017 21:10:54 +0100

Available diffs

• diff from 1.7.1-1 to 1.7.1-2 (595 bytes)

bioperl-run (1.7.1-1) unstable; urgency=medium

  * New upstream version
  * Testsuite: autopkgtest-pkg-perl
  * cme fix dpkg-control
  * Enable lots of tests
  * Module Bio::Tools::Run::WrapperBase was taken over from BioPerl into
    bioperl-run in commit acd57a7d14112c5fd2cd979005b072efdaf57679 which is
    taken over in quilt patch
  * Fix homepage
  * d/watch:
     - version=4
     - Fix versionmangling
  * Build-Depends: raxml
  * Update copyright
  * debhelper 10

 -- Andreas Tille <email address hidden>  Wed, 21 Dec 2016 21:24:05 +0100

Available diffs

• diff from 1.6.9-3 to 1.7.1-1 (241.6 KiB)

bioperl-run (1.6.9-3) unstable; urgency=medium

  [ Charles Plessy ]
  * Build-depend on libmodule-build-perl, Closes: #788888.

  [ Andreas Tille ]
  * Compliant with Standards-Version: 3.9.6

 -- Charles Plessy <email address hidden>  Tue, 23 Jun 2015 20:05:10 +0900

Available diffs

• diff from 1.6.9-2 to 1.6.9-3 (678 bytes)

bioperl-run (1.6.9-2) unstable; urgency=low


  * debian/source/format: 3.0 (quilt)
  * debian/control:
     - cme fix dpkg-control
     - canonical Vcs URLs
     - debhelper 9
  * debian/README.source: removed because redundant
  * debian/copyright: DEP5
  * debian/watch: Point download location to github which provides more
    reliable version numbering than CPAN which would have needed a more
    complex version mangling
  * refreshed quilt patches to get rid of fuzz

 -- Andreas Tille <email address hidden>  Fri, 15 Nov 2013 10:03:29 +0100

Available diffs

• diff from 1.6.9-1 (in Ubuntu) to 1.6.9-2 (5.9 KiB)

bioperl-run (1.6.9-1) unstable; urgency=low

  * New upstream release. 
  * Converted and validated debian/copyright to latest machine-readable format.
  * debian/control:
    - Refreshed the list of packages for which wrappers are provided, in the
      Suggests field as well as in an experimental Build-Recommends field.
    - 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.
  * Point debian/watch to CPAN.
  * Tiny style with Debhelper 8 (debian/rules, debian/compat, debian/control).
  * Split scripts in bioperl-run and modules in libbio-perl-run-perl.
    (debian/rules, debian/control, debian/bioperl-run.install,
    debian/libbio-perl-run-perl.install)
  * debian/rules, debian/patches/series, debian/control:
    - debian/patches/install-scripts.patch for non-interactive script install.
    - debian/patches/Use-system-s-Perl.patch against /usr/local/bin/perl.
    - debian/patches/Some-spellchecking.patch.
  * Trigger network tests with DEB_MAINTAINER_MODE (debian/rules,
    debian/README.test).
 -- Ubuntu Archive Auto-Sync <email address hidden>   Sun,  19 Jun 2011 03:56:48 +0000

Available diffs

• diff from 1.6.1-1 to 1.6.9-1 (2.0 MiB)

bioperl-run (1.6.1-1) unstable; urgency=low

  * New upstream release.
  * debian/patches/10-wrong-path-for-interpreter.patch: removed
    (fixed upstream).
  * debian/watch updated (bioperl -> BioPerl).
  * debian/rules refreshed with dh-make-perl 0.53.
    - Disabled installation of examples (removed upstream).
    - Removed the correction of file permission of Pise documentation
      (removed upstream).
    - Removed patching facilities (no patches anymore).
    - Disabled tests as I experience failures with t/Eponine.t despite
      this program is not installed.
  * debian/copyright:
    - Removed vanity lines about debianization and debian copyright.
    - Incremented years to 2009.
    - Updated to latest experimentation of the machine-readable license summary.
  * debian/control:
    - Incremented Standards-Version to reflect conformance on new Policy
      (dropped versionned build-dependancy on Perl).
    - Removed build-dependancy on quilt (no patches anymore).
    - Depend and Build-Depend on bioperl versions superior or equal to 1.6.0.
    - Build-depends on, and Recommdnes libalgorithm-diff-perl, libipc-run-perl,
      libio-string-perl and libxml-twig-perl, that are listed in DEPENDANCIES.
    - Build-depends on libarray-compare-perl and libtree-dagnode-perl
      (otherwise tests fail). 
    - Depend on amap-align instead of amap (Closes: #541274).

 -- Ubuntu Archive Auto-Sync <email address hidden>   Wed,  04 Nov 2009 01:48:15 +0000

Available diffs

• diff from 1.5.2.100-1 to 1.6.1-1 (945.4 KiB)

bioperl-run (1.5.2.100-1) unstable; urgency=low

  * Initial Release (Closes: #505112).

 -- Ubuntu Archive Auto-Sync <email address hidden>   Thu,  11 Dec 2008 00:48:04 +0000