Change log for bioperl-run package in Ubuntu
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bioperl-run (1.7.3-11) unstable; urgency=medium
* d/control: restrict emboss build-dependency.
emboss is not available anymore on 32-bit and big endian architectures.
It is thus not possible anymore to test it in such context.
* d/control: demote bioperl-run recommends to suggestions.
emboss, hmmer and infernal are currently not available on some release
architectures. Demoting them helps getting the autodep8 perl test
back on tracks at least on s390x.
* d/control: demote tigr-glimmer to suggestion.
* d/control: also restrict tigr-glimmer build-deps architecture set.
-- Étienne Mollier <email address hidden> Sat, 27 Apr 2024 21:48:57 +0200
Available diffs
- diff from 1.7.3-9 to 1.7.3-11 (1.7 KiB)
| Superseded in oracular-release |
| Published in noble-release |
| Published in mantic-release |
| Published in lunar-release |
| Deleted in lunar-proposed (Reason: Moved to lunar) |
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)
| Superseded in lunar-release |
| Obsolete in kinetic-release |
| Published in jammy-release |
| Deleted in jammy-proposed (Reason: Moved to jammy) |
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)
| Superseded in jammy-release |
| Obsolete in impish-release |
| Obsolete in hirsute-release |
| Deleted in hirsute-proposed (Reason: moved to Release) |
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)
| Superseded in hirsute-release |
| Obsolete in groovy-release |
| Deleted in groovy-proposed (Reason: moved to Release) |
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)
| Superseded in groovy-release |
| Published in focal-release |
| Deleted in focal-proposed (Reason: moved to Release) |
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)
| Superseded in focal-release |
| Deleted in focal-proposed (Reason: moved to Release) |
| Deleted in eoan-proposed (Reason: moved to focal-proposed) |
| Deleted in disco-proposed (Reason: moved to eoan-proposed) |
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)
| Superseded in focal-release |
| Obsolete in eoan-release |
| Obsolete in disco-release |
| Deleted in disco-proposed (Reason: moved to release) |
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)
| Superseded in disco-release |
| Obsolete in cosmic-release |
| Deleted in cosmic-proposed (Reason: moved to release) |
| Deleted in bionic-proposed (Reason: Moved to cosmic-proposed.) |
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
| Superseded in cosmic-release |
| Published in bionic-release |
| Obsolete in artful-release |
| Obsolete in zesty-release |
| Deleted in zesty-proposed (Reason: moved to release) |
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)
| Superseded in zesty-release |
| Obsolete in yakkety-release |
| Published in xenial-release |
| Obsolete in wily-release |
| Deleted in wily-proposed (Reason: moved to release) |
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)
| Superseded in wily-release |
| Obsolete in vivid-release |
| Obsolete in utopic-release |
| Published in trusty-release |
| Deleted in trusty-proposed (Reason: moved to release) |
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)
| Superseded in trusty-release |
| Obsolete in saucy-release |
| Obsolete in raring-release |
| Obsolete in quantal-release |
| Published in precise-release |
| Obsolete in oneiric-release |
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)
| Superseded in oneiric-release |
| Obsolete in natty-release |
| Obsolete in maverick-release |
| Obsolete in lucid-release |
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
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