spades (4.0.0+dfsg1-1) experimental; urgency=medium * Team upload * New upstream version 4.0.0+dfsg1 * Refreshing patches * Raising Standards version to 4.7.0 (no change) * Rewriting d/copyright * Changing the paths of the files to remove when repacking * Updating the list of files to exclude when repacking * Updating files related to shipped doc in the debian/ directory * Removing the now useless override of dh_installchangelogs * Using bamtools, googletest, spoa, boost, cuckoo, joblib and xxhash from the Debian packages instead of embedded copies, updating d/control accordingly * Updating paths in d/rules * Adding missing files to the CMakeLists.txt file of the samtools part * Deactivating build-time tests of which test data have vanished from the source package * Updating homepage URI * Removing obsolete Lintian override for source-is-missing * Adding a Lintian override for the embedded (modified) copy of Zlib -- Pierre Gruet Wed, 02 Oct 2024 08:56:41 +0200 spades (3.15.5+dfsg-7) unstable; urgency=medium * Replace distutils which is removed in Python3.12 Closes: #1061846 * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) * Depends: s/python3-distutils/python3-packaging/ -- Andreas Tille Fri, 02 Feb 2024 09:16:42 +0100 spades (3.15.5+dfsg-6) unstable; urgency=medium * d/rules: disable lto builds. Upstream is aware that there is a problem with lto appllied on spades, and this seems to be caused by a lingering compiler bug. (Closes: #1015668) -- Étienne Mollier Sun, 03 Dec 2023 14:52:02 +0100 spades (3.15.5+dfsg-5) unstable; urgency=medium [ Heinrich Schuchardt ] * Add missing libzstd-dev build dependency Closes: #1052315 (LP: #2036726) [ Andreas Tille ] * Standards-Version: 4.6.2 (routine-update) -- Andreas Tille Thu, 21 Sep 2023 13:22:20 +0200 spades (3.15.5+dfsg-4) unstable; urgency=medium * d/control: spades is AMD64 only, as per upstream. Closes: #976523 * d/patches: mark many as not needing forwarding -- Michael R. Crusoe Wed, 09 Aug 2023 12:45:25 +0200 spades (3.15.5+dfsg-3) unstable; urgency=medium * Team upload. * Add fix-gcc13.patch to fix gcc-13 build issues. (Closes: #1037863) -- Bo YU Thu, 20 Jul 2023 21:38:50 +0800 spades (3.15.5+dfsg-2) unstable; urgency=medium * d/control: add missing build-deps following llvm reorganization. (Closes: #1022309) * yaml_load.patch: update to fix new pyyaml.load calls. (Closes: #1022086) * d/copyright: bump copyright year. -- Étienne Mollier Sun, 23 Oct 2022 16:59:13 +0200 spades (3.15.5+dfsg-1) unstable; urgency=medium * New upstream version 3.15.5+dfsg * d/patches/: + fix-privacy-breaches.patch: update badges list. + python3.patch: refresh. + 0003_accept-system-bwa.patch: unfuzz. + yaml_load.patch: unfuzz. * d/m/coronaspades.1.adoc: add manual page for coronaspades. * d/links: create a link for coronaspades.py manual. * d/t/run-upstreams-tests: add self tests for plasmidspades and coronaspades. Also, the truspades command is deprecated, so don't make it's self-test failure critical. * d/salsa-ci.yml: disable run for i386 architecture. * d/NEWS: forward deprecation of truspades with notice it may not work well. -- Étienne Mollier Mon, 01 Aug 2022 21:11:59 +0200 spades (3.15.4+dfsg-3) unstable; urgency=medium * d/t/run-upstreams-tests: make tests a bit more verbose. * Adjust 0003_accept-system-bwa.patch: import support functions. (Closes: #1011968) * Refresh yaml_load.patch. * Remove patches not part of d/p/series anymore. * Add fix-privacy-breaches.patch: remove build status badges. * Add typos.patch: fix typos caught by lintian. * d/copyright: reorder to match globbing properly. * d/s/lintian-overrides: unclear why html files are missing source code. * Standards-Version: 4.6.1 (routine-update) -- Étienne Mollier Sat, 25 Jun 2022 17:41:51 +0200 spades (3.15.4+dfsg-2) unstable; urgency=medium * Team upload. [ Lance Lin ] * d/patches/0003_accept-system-bwa.patch - refactored 'which' Closes: #1010788 [ Andreas Tille ] * Review copyright -- Lance Lin Tue, 10 May 2022 20:15:40 +0700 spades (3.15.4+dfsg-1) unstable; urgency=medium [ Michael R. Crusoe ] * New upstream version * Refreshed patches * debian/upstream/metadata: Added many missing papers * remove assembler/ext/src/llvm/ConvertUTF.cpp * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) [ Steffen Moeller ] * d/u/metadata - yamllint cleanliness - added ref to bioconda * Add salsa-ci file (routine-update) * Refer to common license file for Apache-2.0. * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. * Upstream addressed / -> // in generate_quality (less nice, though) * Prepared PRs for spelling errors found by Michael [ Andreas Tille ] * Adjust patches * Remove redundant gbp.conf [ Juhani Numminen ] * Enable parallel builds by ignoring spades_compile.sh - Fix patches for the bypassing of spades_compile.sh * Remove gcc7.patch: applied upstream * python3.patch: add coronaspades.py and before_start_stage.py * Simplify debian/rules: do not attempt to run as-installed tests before installation * Install scripts under FHS-compliant path /usr/libexec/spades/ - Adjust 0118_adjust_spades_home_again.patch * Add patches to make the test suite runnable * d/links: Add new binary coronaspades(.py) * Remove unused adapt_to_debian_pathes.patch * Add d/clean for test artifacts * Add disable_local_convertutf.patch: to cover for dfsg-removed ConvertUTF.o, link against system's LLVMSupport.a * Build-Deps: does not build python extensions; s/python3-dev/python3-all/ * Depends: remove explicit shared libs (handled as ${shlibs:Depends}) * Use vendored boost which has local modifications to avoid include problems during program use. [ Étienne Mollier ] * Add fix-sigill-on-non-popcnt-cpus.patch; fixes baseline violation. [ Andreas Tille ] * d/watch: - Fix to detect new versions on github (routine-update) - Use proper filename for download * Standards-Version: 4.6.0 (routine-update) * Remove constraints unnecessary since buster: + Build-Depends: Drop versioned constraint on asciidoctor. [ Étienne Mollier ] * Adjust fix-sigill-on-non-popcnt-cpus.patch to not overflow on large int. * d/control: add myself to Uploaders. -- Étienne Mollier Mon, 11 Apr 2022 21:30:33 +0200 spades (3.13.1+dfsg-2) unstable; urgency=medium * Depends: python3-distutils -- Andreas Tille Fri, 22 Nov 2019 10:48:44 +0100 spades (3.13.1+dfsg-1) unstable; urgency=medium * Fix watch file * Moved packaging to Python3 Closes: #938521 * New upstream version * debhelper-compat 12 * Standards-Version: 4.4.1 * Move source package lintian overrides to debian/source. * Set upstream metadata fields: Repository. * Make sure Python3 interpreter is used in scripts * Specify yaml loader * Drop webvis dir from source which has compressed JS but its not used in the binary package -- Andreas Tille Mon, 18 Nov 2019 15:34:43 +0100 spades (3.13.0+dfsg2-2) unstable; urgency=medium * Also remove jemalloc from (build-)depends. -- Michael R. Crusoe Thu, 17 Jan 2019 10:12:47 -0800 spades (3.13.0+dfsg2-1) unstable; urgency=medium * Restore the bundled jemalloc as Debian's package is too new. * Pull releases from GitHib. * Standards-Version: 4.3.0 (no changes needed) * Install README.md to /usr/share/doc/spades/ -- Michael R. Crusoe Thu, 17 Jan 2019 07:54:34 -0800 spades (3.13.0+dfsg-1) unstable; urgency=medium * New upstream version * Upstream has removed dipspades -- Andreas Tille Tue, 16 Oct 2018 22:08:43 +0200 spades (3.12.0+dfsg-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version Closes: #897867 * Fix watch file * Add dh-python [ Alexandre Mestiashvili ] * Add tmp link for tests for spades-bwa * Update override_dh_auto_test: implement a workaround so dh_auto_test can access data files * Add bwa to d/tests/control * Remove *.pyc files * Add patch 0118_adjust_spades_home_again.patch replacing 0113_adjust_paths.patch * Update d/patches/spelling * Remove duplicated docs from /usr/share/spades * Bump Policy to 4.2.1, add myself to uploaders * Use https for copyright Format field, s/MIT/Expat/ * Rename overridden tag to debian-watch-does-not-check-gpg-signature -- Alexandre Mestiashvili Mon, 10 Sep 2018 19:37:49 +0000 spades (3.11.1+dfsg-2) unstable; urgency=medium * Build-Depends: libnlopt-cxx-dev Closes: #902592 * d/rules: + filter nocheck,$(DEB_BUILD_OPTIONS) + do not parse d/changelog * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 -- Andreas Tille Fri, 06 Jul 2018 10:54:09 +0200 spades (3.11.1+dfsg-1) unstable; urgency=medium [ Sascha Steinbiss ] * New upstream release. * Bump Standards-Version. * Remove obsolete Testsuite: entry in d/control * Add d/copyright entry for new included BBHash headers. [ Steffen Moeller ] * debian/upstream/metadata: - added references to registries - yamllint cleanliness -- Sascha Steinbiss Mon, 18 Dec 2017 00:29:26 +0000 spades (3.10.1+dfsg-3) unstable; urgency=medium * Fix FTBFS with GCC 7. Closes: #853666 * Update homepage. * Bump Standards-Version. -- Sascha Steinbiss Thu, 10 Aug 2017 16:39:50 +0200 spades (3.10.1+dfsg-2) unstable; urgency=medium * Upload to unstable. -- Sascha Steinbiss Sun, 18 Jun 2017 16:31:57 +0000 spades (3.10.1+dfsg-1) experimental; urgency=medium [ Michael R. Crusoe ] * New upstream version 3.10.1+dfsg [ Sascha Steinbiss ] * Build for experimental. -- Sascha Steinbiss Fri, 21 Apr 2017 17:54:15 +0000 spades (3.9.1+dfsg-1) unstable; urgency=medium * New upstream release. -- Sascha Steinbiss Wed, 07 Dec 2016 06:31:19 +0000 spades (3.9.0+dfsg-1) unstable; urgency=medium * New upstream release. * Add copyright entry for cxxopts. * Add rnaSPAdes manpage, wrappers, tests. -- Sascha Steinbiss Sun, 24 Jul 2016 13:12:31 +0000 spades (3.8.2+dfsg2-1) unstable; urgency=medium * Make sure bundled headers are not used by cleaning orig tarball. -- Sascha Steinbiss Tue, 19 Jul 2016 20:57:51 +0000 spades (3.8.2+dfsg-1) unstable; urgency=medium * New upstream release. * Adapt patches for new upstream code. * Remove unused override. * Build with debug symbols. -- Sascha Steinbiss Mon, 11 Jul 2016 08:39:53 +0000 spades (3.8.1+dfsg-2) unstable; urgency=medium * Stop using embedded libnlopt, libssw and libhat-trie. * Update email addresses. -- Sascha Steinbiss Sat, 02 Jul 2016 17:45:37 +0000 spades (3.8.1+dfsg-1) unstable; urgency=medium * New upstream release. -- Sascha Steinbiss Mon, 13 Jun 2016 09:02:52 +0000 spades (3.8.0+dfsg-1) unstable; urgency=medium * New upstream release. * Drop patches that are no longer necessary. * Update licenses. * Add metaspades and plasmidspades symlinks. * Add man page stubs for metaspades and plasmidspades. * Bump Standards-Version. -- Sascha Steinbiss Sun, 05 Jun 2016 09:56:42 +0000 spades (3.7.1+dfsg-3) unstable; urgency=medium * Force LANG and LANGUAGE to ensure reproducibility. * Enable compiler messages. -- Sascha Steinbiss Thu, 21 Apr 2016 14:44:14 +0000 spades (3.7.1+dfsg-2) unstable; urgency=medium [ Sascha Steinbiss ] * Use asciidoctor instead of ronn for reproducible man pages * enable full hardening * add override for pedantic Lintian msg * use correct YAML module Closes: #818584 [ Afif Elghraoui ] * Replace patch with a sed command to fix python-yaml imports -- Sascha Steinbiss Fri, 18 Mar 2016 14:25:06 +0000 spades (3.7.1+dfsg-1) unstable; urgency=medium * New upstream release. * Add gbp.conf to always use pristine-tar. -- Sascha Steinbiss Sat, 12 Mar 2016 07:23:31 +0000 spades (3.7.0+dfsg-1) unstable; urgency=medium * Make changelog building reproducible. * New upstream release. * Update d/copyright. -- Sascha Steinbiss Wed, 24 Feb 2016 22:02:53 +0000 spades (3.6.2+dfsg-2) unstable; urgency=medium * Use Debian's jemalloc. * Fix spelling issues. * Bump Standards-Version. -- Sascha Steinbiss Mon, 22 Feb 2016 09:27:51 +0000 spades (3.6.2+dfsg-1) unstable; urgency=low * Initial release (Closes: #813988) -- Sascha Steinbiss Sun, 07 Feb 2016 10:21:39 +0000