Change log for bedtools package in Ubuntu
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bedtools (2.31.1+dfsg-2) unstable; urgency=medium * d/clean: new: remove test/getfasta/t.fa.gz.gzi. (Closes: #1043957) -- Étienne Mollier <email address hidden> Mon, 04 Dec 2023 20:13:11 +0100
Available diffs
bedtools (2.30.0+dfsg-2ubuntu0.1) jammy; urgency=medium * Add d/p/515f6df-Remove-compressBound-assertions-PR-1258.patch in support of fixing 'zlib: compressBound() returns an incorrect result on z15'. (LP: #1961427) -- Frank Heimes <email address hidden> Thu, 19 May 2022 09:52:42 +0200
Available diffs
Superseded in noble-release |
Published in mantic-release |
Published in lunar-release |
Obsolete in kinetic-release |
Deleted in kinetic-proposed (Reason: Moved to kinetic) |
bedtools (2.30.0+dfsg-2ubuntu1) kinetic; urgency=medium * Add d/p/515f6df-Remove-compressBound-assertions-PR-1258.patch in support of fixing 'zlib: compressBound() returns an incorrect result on z15'. (LP: #1961427) -- Frank Heimes <email address hidden> Thu, 19 May 2022 09:52:42 +0200
Available diffs
Superseded in kinetic-release |
Published in jammy-release |
Deleted in jammy-proposed (Reason: Moved to jammy) |
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 <email address hidden> Thu, 02 Sep 2021 06:54:44 +0200
Available diffs
- diff from 2.30.0+dfsg-1 to 2.30.0+dfsg-2 (1.3 KiB)
Superseded in jammy-release |
Obsolete in impish-release |
Obsolete in hirsute-release |
Deleted in hirsute-proposed (Reason: moved to Release) |
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 <email address hidden> Wed, 27 Jan 2021 17:26:26 +0100
Available diffs
- diff from 2.29.2+dfsg-6 to 2.30.0+dfsg-1 (37.1 KiB)
bedtools (2.29.2+dfsg-6) unstable; urgency=medium * Team upload. * Repair broken link in run-unit-test script; fixes autopkgtest regression. -- Étienne Mollier <email address hidden> Sun, 17 Jan 2021 12:11:39 +0100
Available diffs
Superseded in hirsute-proposed |
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 <email address hidden> Mon, 04 Jan 2021 13:01:58 +0100
Available diffs
- diff from 2.29.2+dfsg-4 to 2.29.2+dfsg-5 (1020 bytes)
Superseded in hirsute-proposed |
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 <email address hidden> Sun, 20 Dec 2020 19:03:35 +0100
Superseded in hirsute-release |
Obsolete in groovy-release |
Deleted in groovy-proposed (Reason: moved to Release) |
bedtools (2.29.2+dfsg-3build2) groovy; urgency=medium * No-change rebuild because 2.29.2+dfsg-3(build1) was published in Ubuntu before. -- Logan Rosen <email address hidden> Sat, 09 May 2020 17:12:23 -0400
Available diffs
Superseded in groovy-release |
Published in focal-release |
Deleted in focal-proposed (Reason: moved to Release) |
bedtools (2.27.1+dfsg-4ubuntu1) focal; urgency=medium * Build using python2. -- Matthias Klose <email address hidden> Thu, 02 Apr 2020 11:32:09 +0200
Available diffs
Deleted in focal-proposed (Reason: Debian #955403, remove bedtools from proposed, ftbfs on 3...) |
bedtools (2.29.2+dfsg-3build1) focal; urgency=medium * No-change rebuild for libgcc-s1 package name change. -- Matthias Klose <email address hidden> Mon, 23 Mar 2020 10:25:33 +0100
Available diffs
Superseded in focal-proposed |
bedtools (2.29.2+dfsg-3) unstable; urgency=medium * Team upload. * Build on any architecture -- Michael R. Crusoe <email address hidden> Fri, 14 Feb 2020 16:02:39 +0100
Available diffs
- diff from 2.29.2+dfsg-2 to 2.29.2+dfsg-3 (501 bytes)
Superseded in focal-proposed |
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 <email address hidden> Tue, 11 Feb 2020 16:30:06 +0100
Available diffs
- diff from 2.29.2+dfsg-1 to 2.29.2+dfsg-2 (1.8 KiB)
Superseded in focal-proposed |
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 <email address hidden> Sat, 18 Jan 2020 01:44:47 +0100
Available diffs
- diff from 2.29.0+dfsg-2 to 2.29.2+dfsg-1 (16.6 KiB)
Superseded in focal-proposed |
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 <email address hidden> Thu, 05 Dec 2019 12:11:59 +0100
Available diffs
- diff from 2.29.0+dfsg-1 to 2.29.0+dfsg-2 (4.4 KiB)
Superseded in focal-proposed |
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 <email address hidden> Tue, 05 Nov 2019 21:41:22 +0100
Available diffs
- diff from 2.28.0+dfsg1-1 to 2.29.0+dfsg-1 (182.5 KiB)
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 <email address hidden> Sun, 01 Sep 2019 11:14:59 +0200
Available diffs
Superseded in eoan-proposed |
bedtools (2.28.0+dfsg-3) unstable; urgency=medium * And another new dependency on liblzma-dev -- Steffen Moeller <email address hidden> Fri, 26 Jul 2019 19:06:23 +0200
Superseded in focal-release |
Obsolete in eoan-release |
Obsolete in disco-release |
Deleted in disco-proposed (Reason: moved to release) |
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 <email address hidden> Thu, 14 Feb 2019 22:11:21 +0900
Available diffs
- diff from 2.27.1+dfsg-3 to 2.27.1+dfsg-4 (838 bytes)
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 <email address hidden> Mon, 04 Feb 2019 05:33:48 -0800
Available diffs
- diff from 2.27.1+dfsg-2 to 2.27.1+dfsg-3 (4.3 KiB)
Superseded in disco-release |
Deleted in disco-proposed (Reason: moved to release) |
Deleted in cosmic-proposed (Reason: Moved to disco-proposed) |
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 <email address hidden> Tue, 22 May 2018 21:31:56 +0200
Available diffs
- diff from 2.26.0+dfsg-5 to 2.27.1+dfsg-2 (208.5 KiB)
- diff from 2.27.1+dfsg-1 to 2.27.1+dfsg-2 (1.9 KiB)
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 <email address hidden> Sat, 10 Feb 2018 10:54:56 +0100
Available diffs
- diff from 2.26.0+dfsg-5 to 2.27.1+dfsg-1 (207.3 KiB)
Superseded in disco-release |
Obsolete in cosmic-release |
Published in bionic-release |
Deleted in bionic-proposed (Reason: moved to release) |
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 <email address hidden> Tue, 26 Sep 2017 22:42:08 +0900
Available diffs
- diff from 2.26.0+dfsg-3 to 2.26.0+dfsg-5 (3.0 KiB)
Superseded in bionic-release |
Obsolete in artful-release |
Obsolete in zesty-release |
Deleted in zesty-proposed (Reason: moved to release) |
bedtools (2.26.0+dfsg-3) unstable; urgency=medium d6d3452 Sync with upstream repo at commit 6bf23c, closes: #831833. -- Charles Plessy <email address hidden> Sat, 05 Nov 2016 21:48:09 +0900
Available diffs
- diff from 2.25.0-1 to 2.26.0+dfsg-3 (112.0 KiB)
- diff from 2.26.0+dfsg-2 to 2.26.0+dfsg-3 (49.6 KiB)
bedtools (2.26.0+dfsg-2) unstable; urgency=medium * Enable reproducible builds Closes: #834110 -- Andreas Tille <email address hidden> Fri, 12 Aug 2016 15:04:19 +0200
Available diffs
- diff from 2.26.0+dfsg-1 to 2.26.0+dfsg-2 (670 bytes)
Superseded in yakkety-proposed |
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 <email address hidden> (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 <email address hidden> Thu, 07 Jul 2016 13:58:08 +0900
Superseded in zesty-release |
Obsolete in yakkety-release |
Published in xenial-release |
Deleted in xenial-proposed (Reason: moved to release) |
bedtools (2.25.0-1) unstable; urgency=medium e37865 Merge tag 'v2.25.0' into debian/unstable -- Charles Plessy <email address hidden> Fri, 04 Sep 2015 16:55:21 +0200
Available diffs
- diff from 2.24.0-2 to 2.25.0-1 (1.1 MiB)
Superseded in xenial-release |
Obsolete in wily-release |
Deleted in wily-proposed (Reason: moved to release) |
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 <email address hidden>) Closes: #791830 -- Andreas Tille <email address hidden> Thu, 16 Jul 2015 14:33:38 +0200
Available diffs
- diff from 2.21.0-1 to 2.24.0-2 (13.3 MiB)
- diff from 2.24.0-1 to 2.24.0-2 (2.8 KiB)
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 <email address hidden> Tue, 07 Jul 2015 18:21:22 +0200
Superseded in wily-release |
Obsolete in vivid-release |
Deleted in vivid-proposed (Reason: moved to release) |
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 <email address hidden> Tue, 23 Sep 2014 18:48:17 +0900
Available diffs
- diff from 2.20.1-1 to 2.21.0-1 (52.0 KiB)
Superseded in vivid-release |
Obsolete in utopic-release |
Deleted in utopic-proposed (Reason: moved to release) |
bedtools (2.20.1-1) unstable; urgency=medium * New upstream version * Fix permission of some genome example files -- Andreas Tille <email address hidden> Fri, 06 Jun 2014 21:50:39 +0200
Available diffs
- diff from 2.19.1-2 to 2.20.1-1 (111.5 KiB)
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 <email address hidden> Fri, 09 May 2014 09:48:05 +0200
Available diffs
- diff from 2.19.1-1 to 2.19.1-2 (2.9 KiB)
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 <email address hidden> Fri, 21 Mar 2014 14:51:44 +0900
Available diffs
- diff from 2.17.0-1 to 2.19.1-1 (1.4 MiB)
Superseded in utopic-release |
Published in trusty-release |
Obsolete in saucy-release |
Obsolete in raring-release |
Deleted in raring-proposed (Reason: moved to release) |
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 <email address hidden> Sun, 04 Nov 2012 17:59:41 +0900
Available diffs
- diff from 2.16.1-1 to 2.17.0-1 (254.4 KiB)
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 <email address hidden> Fri, 16 Mar 2012 19:06:49 +0900
Available diffs
- diff from 2.14.3-1 (in Ubuntu) to 2.16.1-1 (264.9 KiB)
bedtools (2.14.3-1) unstable; urgency=low [04f6aa3] Bugfix release.
Available diffs
- diff from 2.13.3-1ubuntu1 to 2.14.3-1 (15.0 KiB)
Superseded in precise-release |
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 <email address hidden> Mon, 17 Oct 2011 21:30:47 +0100
Available diffs
- diff from 2.13.3-1 to 2.13.3-1ubuntu1 (736 bytes)
bedtools (2.13.3-1) unstable; urgency=low [ea1c596] New upstream release.
Available diffs
- diff from 2.12.0-1 to 2.13.3-1 (174.2 KiB)
bedtools (2.12.0-1) unstable; urgency=low * Initial release (Closes: #629597) -- Ubuntu Archive Auto-Sync <email address hidden> Thu, 09 Jun 2011 11:26:45 +0000
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