abyss (2.3.10-1) unstable; urgency=medium * New upstream version 2.3.10 * fix-privacy-breach.patch: refresh. * d/manpages: install abyss-pe.1. * abyss-pe.patch: declare forwarding not needed. -- Étienne Mollier Sat, 02 Nov 2024 14:00:42 +0100 abyss (2.3.9-1) unstable; urgency=medium * New upstream version 2.3.9 (Closes: #1080071) * fix-privacy-breach.patch: refresh. -- Étienne Mollier Thu, 12 Sep 2024 22:44:04 +0200 abyss (2.3.8-1) unstable; urgency=medium [ Michael R. Crusoe ] * d/control: simplify architecture specifications by using provisions from the architecture-properties package. [ Étienne Mollier ] * New upstream version 2.3.8 * fix-privacy-breach.patch: freshen. * d/copyright: bump copyright years. * d/control: declare compliance to standards version 4.7.0. * d/{control,rules}: migrate from pkg-config to pkgconf. -- Étienne Mollier Sat, 27 Jul 2024 18:59:57 +0200 abyss (2.3.7-3) unstable; urgency=medium * Add build support for loongarch64 Closes: #1058457 -- Andreas Tille Sat, 16 Dec 2023 18:14:36 +0100 abyss (2.3.7-2) unstable; urgency=medium [ Andreas Tille ] * btllib code is now external [ Étienne Mollier ] * d/rules: build with -Wno-error=dangling-reference. This fixes build failures with gcc 13. (Closes: #1050557) -- Étienne Mollier Sat, 26 Aug 2023 12:20:49 +0200 abyss (2.3.7-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.6.2 (routine-update) * Build-Depends: libbtllib-dev -- Andreas Tille Mon, 03 Jul 2023 13:51:37 +0200 abyss (2.3.5+dfsg-2) unstable; urgency=medium * d/control: add myself to uploaders. * d/watch: switch to git mode; fixes github scan. -- Étienne Mollier Sat, 22 Oct 2022 12:56:40 +0200 abyss (2.3.5+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version * Standards-Version: 4.6.1 (routine-update) * Add fix-privacy-breach.patch; this is to avoid pinging a badges server while reading the offline documentation. -- Étienne Mollier Sat, 14 May 2022 14:19:36 +0200 abyss (2.3.4+dfsg-1) unstable; urgency=medium * Upstream declares that only 64bit architectures are supported (https://github.com/bcgsc/abyss/issues/384) thus restricting architectures accordingly Closes: #1000577 * Exclude i386 from salsa-ci * New upstream version * Add missing build dependency on dh addon. * Exclude external files from RResolver/btllib/external/sdsl-lite -- Andreas Tille Fri, 14 Jan 2022 09:36:02 +0100 abyss (2.3.3-2) unstable; urgency=medium * Fix autopkgtest * Use gzipped data files in source package -- Andreas Tille Tue, 16 Nov 2021 08:11:26 +0100 abyss (2.3.3-1) unstable; urgency=medium * No need to exclude files any more * Make sure target dir for manpages exists * New upstream version -- Andreas Tille Mon, 15 Nov 2021 13:14:45 +0100 abyss (2.3.1-1) unstable; urgency=medium * Fix watchfile to detect new versions on github * New upstream version * Standards-Version: 4.6.0 (routine-update) -- Andreas Tille Fri, 01 Oct 2021 16:10:22 +0200 abyss (2.2.5+dfsg-1) unstable; urgency=medium * s/bsdmainutils/bsdextrautils/ Required for abyss-tabtomd, which needs /usr/bin/column Closes: #964532 * Standards-Version: 4.5.1 (routine-update) * Remove default debian/gbp.conf * Remove unneeded docs of btllib since these contain compressed JS -- Andreas Tille Fri, 04 Dec 2020 14:42:34 +0100 abyss (2.2.5-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) -- Andreas Tille Thu, 01 Oct 2020 13:24:22 +0200 abyss (2.2.4-1) unstable; urgency=medium * New upstream version * spelling patch incorporated upstream, removed it * Remove markdown from the nodoc build profile, to allow for cross-building -- Michael R. Crusoe Tue, 11 Feb 2020 15:39:45 +0100 abyss (2.2.3-2) unstable; urgency=medium * Use libtext-multimarkdown-perl to obtain html documentation Closes: #942908 * Standards-Version: 4.4.1 -- Andreas Tille Sun, 15 Dec 2019 00:00:48 +0100 abyss (2.2.3-1) unstable; urgency=medium * New upstream version * Remove strict-alignment patch as per upstream: "Adding an additionally memcpy would slow down these inner-loop functions. Architectures without hardware support for unaligned memory access are currently unsupported by ABySS." https://github.com/bcgsc/abyss/pull/279#issuecomment-468079889 * Turn off the 32-bit patch for now. Local testing with i386 shows that it may not be needed as suggested by upstream. -- Michael R. Crusoe Sat, 28 Sep 2019 12:04:53 +0200 abyss (2.2.2-1) unstable; urgency=medium * New upstream version -- Michael R. Crusoe Sat, 17 Aug 2019 08:53:07 +0200 abyss (2.2.1-1) unstable; urgency=medium * New upstream release, should fix failing builds on 32-bit architectures. * Remove unused libgtest-dev dependency, as it is unused and may be causing an error on hurd * debhelper-compat 12 * Standards-Version: 4.4.0 * Use secure URI in debian/watch. * Set upstream metadata fields: Contact. -- Michael R. Crusoe Tue, 13 Aug 2019 12:38:14 +0200 abyss (2.2.0-1) unstable; urgency=medium * New upstream. * Several patches incorporated upstream and removed * Merged upstream's copyright file with debian/copyright -- Michael R. Crusoe Thu, 08 Aug 2019 16:48:50 +0200 abyss (2.1.5-7) unstable; urgency=medium * Add myself as an uploader. * The package openmpi-bin is now a required dependency for the abyss binary package. Many thanks to ci.debian.org for bringing this to light. * Fix "implicit declaration of function"s in dialign/museq.c * Fix some spelling typos * Register the flowchart PDFs with doc-base -- Michael R. Crusoe Sun, 17 Feb 2019 05:19:54 -0800 abyss (2.1.5-6) unstable; urgency=high * Team upload. * Add dependency on openmpi-common for error messages -- Michael R. Crusoe Sat, 16 Feb 2019 01:52:28 -0800 abyss (2.1.5-5) unstable; urgency=medium * Team upload. * Fix MPI build. Closes: #922351 -- Michael R. Crusoe Fri, 15 Feb 2019 06:23:47 -0800 abyss (2.1.5-4) unstable; urgency=medium * Fix build on hurd due to missing header file (thanks for the patch to Samuel Thibault ) Closes: #920240 * debhelper 12 -- Andreas Tille Wed, 23 Jan 2019 15:49:21 +0100 abyss (2.1.5-3) unstable; urgency=medium * Re-add armel architecture Closes: #918735 -- Andreas Tille Wed, 09 Jan 2019 21:23:43 +0100 abyss (2.1.5-2) unstable; urgency=medium * Restrict set of architectures to those where package is known to build (or never was successfully build) Closes: #918575 * Standards-Version: 4.3.0 -- Andreas Tille Tue, 08 Jan 2019 15:53:09 +0100 abyss (2.1.5-1) unstable; urgency=medium * Fix strict alignment violation on sparc64 (Thanks to David Matthew Mattli and James Clarke) Closes: #889147 * New upstream version * Remove trailing whitespace in debian/changelog * Remove trailing whitespace in debian/copyright -- Andreas Tille Sat, 08 Dec 2018 07:24:02 +0100 abyss (2.1.1-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.2.1 * Fix Perl interpreter path -- Andreas Tille Wed, 26 Sep 2018 13:30:44 +0200 abyss (2.1.0-1) unstable; urgency=medium * New upstream version * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 -- Andreas Tille Fri, 20 Apr 2018 10:04:32 +0200 abyss (2.0.3-1) unstable; urgency=medium [ Steffen Moeller ] * debian/upstream/metadata: RRID -> SciCrunch [ Andreas Tille ] * New upstream version * Standards-Version: 4.1.3 * debhelper 11 -- Andreas Tille Tue, 20 Mar 2018 14:33:26 +0100 abyss (2.0.2-3) unstable; urgency=medium * Team upload. [ Nadiya Sitdykova ] * Add simple autopkgtest test-suite. [ Steffen Moeller ] * [debian/upstream/metadata] Added references to bio.tools, OMICtools and RRID [ Sascha Steinbiss ] * Add missing dependency on bsdmainutils. * Use HTTPS URL for Format entry in d/copyright. * Bump Standards-Version. -- Nadiya Sitdykova Fri, 30 Jun 2017 16:56:26 -0400 abyss (2.0.2-2) unstable; urgency=medium * FTBFS on mips and other big-endian architectures (Thanks for the patch to Daniel Knezevic ) Closes: #847574 * debhelper 10 * d/watch: version=4 -- Andreas Tille Sun, 11 Dec 2016 14:24:34 +0100 abyss (2.0.2-1) unstable; urgency=medium * New upstream version -- Andreas Tille Tue, 01 Nov 2016 12:06:10 +0100 abyss (2.0.1-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version now licensed under GPL-3 * Moved package to main * cme fix dpkg-control * use markdown to create doc * hardening=+all [ Gert Wollny ] * Force gtest to use c++11 based std::tuple -- Andreas Tille Mon, 10 Oct 2016 19:57:56 +0200 abyss (1.9.0-1) unstable; urgency=medium * New upstream version Adapted patches * Took over COPYRIGHT from upstream as debian/copyright * Dropped Shaun Jackman from Uploaders since he confirmed that he will not be able to maintain the package * Build-Depends: libsqlite3-dev * Script uses bash syntax so request bash interpreter -- Andreas Tille Thu, 16 Jul 2015 11:28:54 +0200 abyss (1.5.2-2) unstable; urgency=medium * abyss-fixmate and DistanceEst are expected to be in /usr/bin by sga * configure was missing ghc -> mention this fact in README.source for further inspection * Fix FTBFS on 32-bit architectures (thanks for the patch to Graham Inggs ) Closes: #780409 * cme fix dpkg-control -- Andreas Tille Mon, 18 May 2015 14:24:21 +0200 abyss (1.5.2-1) unstable; urgency=medium * New upstream version (remove applied patches) * d/watch: Moved to github * d/control+d/rules: use dh-autoreconf * d/control: Build-Depends: libtext-multimarkdown-perl * cme fix dpkg-control * d/control: Build-Depends: libgtest-dev to enable unit tests at build time * d/control: drop copy of citation info from long description * patch to make gtest work (thanks to Anthony Raymond ) * Drop privacy breach in doc -- Andreas Tille Mon, 15 Sep 2014 14:53:24 +0200 abyss (1.3.6-1) unstable; urgency=low * Team upload (Closes: #722072). e05ee57 Imported Upstream version 1.3.5 b391f1f Imported Upstream version 1.3.6 (Closes: #702440) 7edc28b Signal the use of git-buildpackage with this configuration file. a3beaac Normalised source package control file with config-model-edit. dd86394 Conforms with Policy version 3.9.4. 71d42ad Normalised VCS URLs. -- Charles Plessy Sun, 08 Sep 2013 11:36:44 +0900 abyss (1.3.4-4) unstable; urgency=low * Team upload. * Fix FTBFS with gcc-4.8, -Werror=unused-local-typedefs. * Enable parallel build. -- Dmitrijs Ledkovs Mon, 01 Jul 2013 21:06:59 +0100 abyss (1.3.4-3) unstable; urgency=low * Disable POPCNT Closes: #697344 * Add debian/README.debian to inform users about this change asking for some comparison of the speed to consider other means for better performance -- Andreas Tille Fri, 04 Jan 2013 11:07:10 +0100 abyss (1.3.4-2) unstable; urgency=low * Team upload * debian/upstream: BibTeX compliant authors -- Andreas Tille Fri, 01 Jun 2012 08:38:29 +0200 abyss (1.3.4-1) unstable; urgency=low * New upstream release. * debian/copyright: Add CityHash, which has an Expat license. * debian/control: Bump Standards-Version to 3.9.3.1. -- Shaun Jackman Thu, 31 May 2012 11:39:13 -0700 abyss (1.3.3-2) unstable; urgency=low * debian/control: - Team maintenance in Debian Med team - Moved packaging to Git * debian/upstream: Add citation information * debhelper 9 (control+compat) * debian/copyright: Add github as another location for obtaining the source -- Andreas Tille Sun, 01 Apr 2012 08:44:48 +0200 abyss (1.3.3-1) unstable; urgency=low * New upstream release. * Some components are dual-licensed BCCA-Academic or GPL-3+. * Bump Standards-Version to 3.9.3. -- Shaun Jackman Tue, 13 Mar 2012 15:43:49 -0700 abyss (1.3.2-1) unstable; urgency=low * New upstream release. -- Shaun Jackman Tue, 13 Dec 2011 17:04:24 -0800 abyss (1.3.1-1) unstable; urgency=low * New upstream release. -- Shaun Jackman Mon, 24 Oct 2011 11:32:59 -0700 abyss (1.3.0-1) unstable; urgency=low * New upstream release. * Add libboost-graph-dev to Build-Depends. -- Shaun Jackman Sun, 11 Sep 2011 10:00:13 -0700 abyss (1.2.7-3) unstable; urgency=low * Align/Aligner.cpp, Scaffold/scaffold.cc: Fix FTBFS bug for GCC 4.6. -- Shaun Jackman Mon, 15 Aug 2011 11:07:19 -0700 abyss (1.2.7-2) unstable; urgency=low * debian/control: Add `XS-Autobuild: yes'. Suggest openmpi-bin. * debian/copyright: Change `Format-Specification' to `Format'. -- Shaun Jackman Thu, 21 Jul 2011 09:55:52 -0700 abyss (1.2.7-1) unstable; urgency=low * Initial release. Closes: #631534. -- Shaun Jackman Fri, 24 Jun 2011 12:16:36 -0700