bedtools (2.30.0+dfsg-3) unstable; urgency=medium * Do not use ulimit in test Closes: #1034349 * Override false positive (see lintian bug #1017966) -- Andreas Tille Thu, 13 Apr 2023 14:12:15 +0200 bedtools (2.30.0+dfsg-2) unstable; urgency=medium [ Steffen Möller ] * Update metadata - indent, added ref to guix [ Étienne Mollier ] * d/control: add myself to uploaders * d/watch: fix broken link to github [ Andreas Tille ] * Standards-Version: 4.6.0 (routine-update) -- Andreas Tille Thu, 02 Sep 2021 06:54:44 +0200 bedtools (2.30.0+dfsg-1) unstable; urgency=medium [ Étienne Mollier ] * Team upload. * New upstream version 2.30.0+dfsg. * Refresh 2to3.patch and hardening patch. * Remove test related patches, 32-bit-fixes.patch and spelling patch; applied upstream. * Do not include htsutil as a side test program in bedtools anymore; the test tool is inlined as subcommand to reduce memory footprint. [ John Marshall ] * Add htsutil patch to implement the bedtools htsutil subcommand. [ Étienne Mollier ] * d/rules: set $htsutil to use the bedtools htsutil subcommand. * d/t/run-unit-test: use the bedtools htsutil subcommand. -- Étienne Mollier Wed, 27 Jan 2021 17:26:26 +0100 bedtools (2.29.2+dfsg-6) unstable; urgency=medium * Team upload. * Repair broken link in run-unit-test script; fixes autopkgtest regression. -- Étienne Mollier Sun, 17 Jan 2021 12:11:39 +0100 bedtools (2.29.2+dfsg-5) unstable; urgency=medium * Delete standard debian/gbp.conf * Revert deletion of test binary htsutil since it is needed to replace samtools that's not working any more for this purpose * Move htsutil tool to bedtools package Closes: #978679 -- Andreas Tille Mon, 04 Jan 2021 13:01:58 +0100 bedtools (2.29.2+dfsg-4) unstable; urgency=medium [ Michael R. Crusoe ] * Team upload. * Remove the need for samtools via patch from upstream. * Include patch from Bernhard Übelacker to fix 32-bit builds. TODO: the autopkgtests do not yet pass on i386 (and likely neither on other 32-bit archs). Closes: #955403 * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) [ Andreas Tille ] * Fix permissions of .sam files * Delete test binary to make sure it will not be installed * DEP3 * Standards-Version: 4.5.1 (routine-update) -- Andreas Tille Sun, 20 Dec 2020 19:03:35 +0100 bedtools (2.29.2+dfsg-3) unstable; urgency=medium * Team upload. * Build on any architecture -- Michael R. Crusoe Fri, 14 Feb 2020 16:02:39 +0100 bedtools (2.29.2+dfsg-2) unstable; urgency=medium [ Steffen Moeller ] * Team upload. * Added version to dependency of samtools [ Michael R. Crusoe ] * Make the build verbose * Fix a spelling typo * Improve hardening & enable cross building -- Michael R. Crusoe Tue, 11 Feb 2020 16:30:06 +0100 bedtools (2.29.2+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version * Fixed failing intersect.new #78 test as instructed on https://github.com/arq5x/bedtools2/issues/814 * Standard-Version: 4.5.0 -- Steffen Moeller Sat, 18 Jan 2020 01:44:47 +0100 bedtools (2.29.0+dfsg-2) unstable; urgency=medium * Fix Build-Depends (s/python/python3/) and replace remaining references to python by python3 Closes: #936199 * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g * Remove patches louder, reproducible_build.patch that are missing from debian/patches/series. * Set fields Upstream-Contact in debian/copyright. * Remove obsolete fields Contact, Name from debian/upstream/metadata. -- Andreas Tille Thu, 05 Dec 2019 12:11:59 +0100 bedtools (2.29.0+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version * Removed Chris' reproducible builds patch - upstream diverged too much -- Steffen Moeller Tue, 05 Nov 2019 21:41:22 +0100 bedtools (2.28.0+dfsg1-1) unstable; urgency=medium * Use 2to3 to port to Python3 Closes: #936199 * Remove unsafe links for gcc and g++ -- Andreas Tille Sun, 01 Sep 2019 11:14:59 +0200 bedtools (2.28.0+dfsg-3) unstable; urgency=medium * Team upload. * And another new dependency on liblzma-dev -- Steffen Moeller Fri, 26 Jul 2019 19:06:23 +0200 bedtools (2.28.0+dfsg-2) unstable; urgency=medium * Team upload. * Debian CI kindly pointed me to a new build dependency on libbz2-dev (https://salsa.debian.org/med-team/bedtools/-/jobs/238984). -- Steffen Moeller Fri, 26 Jul 2019 18:38:06 +0200 bedtools (2.28.0+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version * debhelper-compat 12 * Standards-Version: 4.4.0 * Semi-automated update with Andreas' routine-update script, only reintroduced the conflicts of the test package with earlier releases of bedtools. -- Steffen Moeller Fri, 26 Jul 2019 17:33:35 +0200 bedtools (2.27.1+dfsg-4) unstable; urgency=medium * Disable the shuffle test on other 32-bit architectures. * Restrict build to little-endian release architectures. Closes: #890117 * QA-build with Salsa. -- Charles Plessy Thu, 14 Feb 2019 22:11:21 +0900 bedtools (2.27.1+dfsg-3) unstable; urgency=medium * Team upload. * Print compilation commands * For *i386: use -ffloat-store; disable shuffle tests. Closes: #890116 * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target * Remove trailing whitespace in debian/changelog * Remove trailing whitespace in debian/copyright * mark bedtools-test as Multi-Arch: foreign -- Michael R. Crusoe Mon, 04 Feb 2019 05:33:48 -0800 bedtools (2.27.1+dfsg-2) unstable; urgency=medium * Team upload [ Andreas Tille ] * Install autopkgtest script as /usr/share/doc/bedtools/run-unit-test * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 * Drop useless get-orig-source target [ Liubov Chuprikova ] * Fix "autopkgtest fails while it succeeded in the past" updated run-unit-test to match new upstream tests Closes: #894781 -- Liubov Chuprikova Tue, 22 May 2018 21:31:56 +0200 bedtools (2.27.1+dfsg-1) unstable; urgency=medium * New upstream version * cme fix dpkg-control * debhelper 11 * d/rules: do not parse d/changelog -- Andreas Tille Sat, 10 Feb 2018 10:54:56 +0100 bedtools (2.26.0+dfsg-5) unstable; urgency=medium * Use "override_dh_install-indep" to prevent failures when architecture-independent packages are not built. Closes: #876802 -- Charles Plessy Tue, 26 Sep 2017 22:42:08 +0900 bedtools (2.26.0+dfsg-4) unstable; urgency=medium [ Andreas Tille ] * Fix autopkgtest * Ignore failures in the split feature for the moment (Related to bug #747337 but hesitating to close it) * debhelper 10 * d/watch: version=4 [Steffen Moeller] * debian/upstream/metadata: Added references to registries * debian/copyright: Added Upstream-Name [ Charles Plessy ] * Distribute /usr/bin/groupBy again. * Conflict/Replace/Provide filo (which is being removed from Debian). -- Charles Plessy Mon, 25 Sep 2017 23:09:53 +0900 bedtools (2.26.0+dfsg-3) unstable; urgency=medium d6d3452 Sync with upstream repo at commit 6bf23c, closes: #831833. -- Charles Plessy Sat, 05 Nov 2016 21:48:09 +0900 bedtools (2.26.0+dfsg-2) unstable; urgency=medium * Enable reproducible builds Closes: #834110 -- Andreas Tille Fri, 12 Aug 2016 15:04:19 +0200 bedtools (2.26.0+dfsg-1) unstable; urgency=medium [ Charles Plessy ] 854dcc2 Merge tag 'v2.26.0' into debian/unstable 99afd11 Ensure the architecture-independent package can be built separately. Thanks to Santiago Vila (Closes: #805998) [ Andreas Tille ] * Switch to default repository layout * Remove docs/content/images/tool-glyphs/barski_binding_site.png from upstream tarball since it is from Jothi et al, 2008, doi:10.1093/nar/gkn488 since it is licensed under no-DFSG CC-BY-NC 2.0 * Delete reference to removed image from Debian shipped doc * cme fix dpkg-control * cme fix dpkg-copyright * hardening += all * drop outdated Homepage field from debian/upstream/metadata * debian/control: Fix homepage -- Charles Plessy Thu, 07 Jul 2016 13:58:08 +0900 bedtools (2.25.0-1) unstable; urgency=medium e37865 Merge tag 'v2.25.0' into debian/unstable -- Charles Plessy Fri, 04 Sep 2015 16:55:21 +0200 bedtools (2.24.0-2) unstable; urgency=medium * Tests need bgzip from tabix package * Add missing input files for tests * link to genomes files in autopkgtests to enable more tests passing * Fix MIPS build issue (Thanks for picking the patch from upstream Arturo Borrero Gonzalez ) Closes: #791830 -- Andreas Tille Thu, 16 Jul 2015 14:33:38 +0200 bedtools (2.24.0-1) unstable; urgency=medium [ Charles Plessy ] b757049 Merge tag 'v2.22.1' into debian/unstable f62bafa Conforms to Policy 3.9.6. [ Andreas Tille ] * Remove superfluous debian/README.source and replace it by a helpful one describing the workflow of this Git archive * New upsteam version * Bash completions now go to /usr/share/bash-completion/completions * Strip executable flag from all *.bed files * Make sure all *.sh scripts of the test suite have a proper '#!/bin/bash' line and the executable flag set * debian/copyright - update download location - turn DEP5 incompatible License field in header into a Comment -- Andreas Tille Tue, 07 Jul 2015 18:21:22 +0200 bedtools (2.21.0-1) unstable; urgency=medium 856a5fd Merge tag 'v2.21.0' into debian/unstable a4f6ab7 Merge corrections on version number. -- Charles Plessy Tue, 23 Sep 2014 18:48:17 +0900 bedtools (2.20.1-1) unstable; urgency=medium * New upstream version * Fix permission of some genome example files -- Andreas Tille Fri, 06 Jun 2014 21:50:39 +0200 bedtools (2.19.1-2) unstable; urgency=medium * debian/tests/control: Add "Depends: @, samtools" as advised in #747337 * debian/tests/upstream: Use content from bedtools-test package to actually run the test suite Closes: #747337 * debian/rules: Use dh to easily enable unit tests at package build time * Build-Depends: samtools to run the full test suite -- Andreas Tille Fri, 09 May 2014 09:48:05 +0200 bedtools (2.19.1-1) unstable; urgency=medium 479e63b Merge tag 'v2.19.1' into debian/unstable [ Charles Plessy ] 93a7cf1 Create autopkgtest testsuite and a new package bedtools-test. 46183f8 debian/copyright: update path, correct license short name. 4fd441a debian/rules: removed obsolete exception of compression. [ James McCoy ] b4fa8e1 Move debian/upstream to debian/upstream/metadata -- Charles Plessy Fri, 21 Mar 2014 14:51:44 +0900 bedtools (2.19.0-1) unstable; urgency=low e07e70c Imported Upstream version 2.19.0 afdc61a Watch GitHub at https://github.com/arq5x/bedtools2. 4abe14e Source control file normalised with config-model-edit. 0518353 Corrected a typo in the long description. (Closes: #714873) f63d85e Follow the layout of the upstream repository. c25f9e5 Correct name of README file in debian/docs. 5561c7c Emulate source format 1.0 in the format 3.0 (quilt). a45a0ab Canonical VCS URLs. 4459dfe Conforms with Policy 3.9.5. -- Charles Plessy Sat, 15 Feb 2014 19:39:23 +0900 bedtools (2.17.0-1) unstable; urgency=low bb9012e Imported Upstream version 2.16.2. 9006b23 Imported Upstream version 2.17.0. 9112569 Documented BEDTools license as a whole. 325689c Removed Pre-Depends: dpkg (>= 1.15.6). a781b14 Conforms with Policy 3.9.4. 84b1167 Use Debhelper 9. 0bf572d Distribute the test suite. 422cd34 Bash completion for BEDTools. -- Charles Plessy Sun, 04 Nov 2012 17:59:41 +0900 bedtools (2.16.1-1) unstable; urgency=low b7f2405 New upstream release. 4add346 Corrected, updated and normalised Debian copyright. 00b426d Conforms to Debian Policy 3.9.3. 72c3c94 Verbose Debhelper. -- Charles Plessy Fri, 16 Mar 2012 19:06:49 +0900 bedtools (2.15.0-1) unstable; urgency=low 3f8e754 Upstream version 2.15.0. f27b295 Build-depend on python because of scripts/makeBashScripts.py. 2e3e8e8 Removed the /usr/bin/groupBy wrapper, as groupBy is also distributed by the filo package. -- Charles Plessy Wed, 11 Jan 2012 15:07:45 +0900 bedtools (2.14.3-1) unstable; urgency=low 04f6aa3 Bugfix release. -- Charles Plessy Fri, 04 Nov 2011 09:25:38 +0900 bedtools (2.14.2-1) unstable; urgency=low 356313d Bugfix release. -- Charles Plessy Thu, 03 Nov 2011 12:15:32 +0900 bedtools (2.14.1-1) unstable; urgency=low bce732c New upstream release and new tool, multiBedIntersect. -- Charles Plessy Thu, 03 Nov 2011 11:14:35 +0900 bedtools (2.13.4-1) unstable; urgency=low e553c37 New upstream release. -- Charles Plessy Sat, 29 Oct 2011 11:08:02 +0900 bedtools (2.13.3-1ubuntu1) precise; urgency=low * Pre-Depends: dpkg (>= 1.15.6) for xz compression support. Needed until after Ubuntu 12.04 LTS. -- Colin Watson Mon, 17 Oct 2011 21:30:47 +0100 bedtools (2.13.3-1) unstable; urgency=low ea1c596 New upstream release. -- Charles Plessy Wed, 05 Oct 2011 17:18:15 +0900 bedtools (2.13.2-1) unstable; urgency=low 1930a26 New upstream release. -- Charles Plessy Sat, 24 Sep 2011 09:34:29 +0900 bedtools (2.13.1-1) unstable; urgency=low 2e3fe5e New upstream release. ff5450e Compress source and binary packages with xz. ef58a33 Suggest filo for the groupBy command. df206c0 Mangle debian/watch download URL. 2fe7cff Simplified repacking as upstream tarballs do not contain ‘*/*DS_Store’ files anymore. -- Charles Plessy Sat, 10 Sep 2011 23:32:43 +0900 bedtools (2.12.0-1) unstable; urgency=low * Initial release (Closes: #629597) -- Charles Plessy Wed, 08 Jun 2011 17:01:19 +0900