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 Sun, 22 Jan 2023 12:26:27 +0100 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 Thu, 10 Feb 2022 20:44:28 +0100 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 Tue, 14 Sep 2021 18:52:51 +0200 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 Wed, 06 Jan 2021 22:38:23 +0100 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 Thu, 03 Dec 2020 21:57:37 +0100 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 Tue, 31 Mar 2020 01:13:25 +0530 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 Tue, 07 Jan 2020 12:07:09 +0100 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 Sat, 04 Jan 2020 17:49:32 +0100 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 ) * Versioned (Build-)Depends: bioperl (>= 1.7.4) -- Andreas Tille Mon, 11 Feb 2019 22:14:53 +0100 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 Fri, 14 Sep 2018 20:10:08 +0200 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 Fri, 26 Jan 2018 10:43:45 +0100 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 Thu, 07 Dec 2017 18:19:04 +0100 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 Wed, 20 Sep 2017 14:29:45 +0200 bioperl-run (1.7.1-3) unstable; urgency=medium * s/Conflicts/Breaks/ Closes: #850029 -- Andreas Tille Fri, 13 Jan 2017 08:25:26 +0100 bioperl-run (1.7.1-2) unstable; urgency=medium * Conflicts: libbio-perl-perl (<< 1.7.1-1) Closes: #850029 -- Andreas Tille Tue, 03 Jan 2017 21:10:54 +0100 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 Wed, 21 Dec 2016 21:24:05 +0100 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 Tue, 23 Jun 2015 20:05:10 +0900 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 Fri, 15 Nov 2013 10:03:29 +0100 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). -- Charles Plessy Sat, 18 Jun 2011 13:21:36 +0900 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). -- Charles Plessy Thu, 03 Sep 2009 11:00:03 +0900 bioperl-run (1.5.2.100-1) unstable; urgency=low * Initial Release (Closes: #505112). -- Charles Plessy Mon, 10 Nov 2008 09:11:17 +0900