seqan2 (2.4.0+dfsg-16) unstable; urgency=medium * Skip test solution_online_search_finder which might break occasionally Closes: #1058548 * Standards-Version: 4.6.2 (routine-update) -- Andreas Tille Mon, 15 Jan 2024 13:57:17 +0100 seqan2 (2.4.0+dfsg-15) unstable; urgency=medium * Fix watch file * Standards-Version: 4.6.1 (routine-update) * Use secure URI in Homepage field. * Set upstream metadata fields: Repository-Browse. [Team upload] * Fix tests against python3 (Closes: #1026492) **pending issue** fixes all tests BUT remains mason2 tests failing for complete different reason -- Andreas Tille Tue, 06 Dec 2022 15:52:21 +0100 seqan2 (2.4.0+dfsg-14) unstable; urgency=medium * Exclude yara build also for i386 -- Andreas Tille Sat, 13 Feb 2021 21:18:04 +0100 seqan2 (2.4.0+dfsg-13) unstable; urgency=medium [ Vagrant Cascadian ] * Enable reproducible=+fixfilepath Closes: #972752 [ Andreas Tille ] * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit. * Install sak.1 manpage -- Andreas Tille Mon, 14 Dec 2020 08:06:32 +0100 seqan2 (2.4.0+dfsg-12) unstable; urgency=medium * Convert python scripts to python3. Closes: #938465 * debhelper-compat 12 * Standards-Version: 4.5.0 * Drop custom source compression. * Remove empty debian/source/options. * Remove obsolete fields Name, Contact from debian/upstream/metadata. -- Michael R. Crusoe Sat, 08 Feb 2020 15:48:08 +0100 seqan2 (2.4.0+dfsg-11) unstable; urgency=medium * Fix Exclusion of tests on armhf and mips -- Andreas Tille Wed, 30 Jan 2019 14:21:53 +0100 seqan2 (2.4.0+dfsg-10) unstable; urgency=medium [ Michael R. Crusoe ] * debian/patches/ia64_yield: Fix thread wait assembly for IA64. Closes: #890185 [ Andreas Tille ] * Ignore two tests on armhf and one test on mips to let the build succeed on these architectures * debhelper 12 * Standards-Version: 4.3.0 -- Andreas Tille Tue, 29 Jan 2019 22:38:30 +0100 seqan2 (2.4.0+dfsg-9) unstable; urgency=medium [ Michael R. Crusoe ] * Generate the CWL descriptions automatically, now that CTDConverter is packaged. (This does not work and was deactivated in favour of fixing bug #892223 quickly.) [ Steve Langasek ] * use alignment-safe buffer handling Closes: #892223 [ Andreas Tille ] * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * Remove trailing whitespace in debian/changelog * Build-Depends: fakeroot (Something is broken since this is not automatically installed. This should not be necessary and should be removed in next revision.) * debian/rules: Fix PATH in attempt to create CWL descriptions -- Andreas Tille Wed, 05 Dec 2018 11:36:39 +0100 seqan2 (2.4.0+dfsg-8) unstable; urgency=medium * Fix AutoPkgTests. Miscellaneous cleanups of debian/rules. * Use seperate build directory for the -dev package so we can run cmake with -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY -- Michael R. Crusoe Mon, 19 Feb 2018 02:15:18 -0800 seqan2 (2.4.0+dfsg-7) unstable; urgency=medium * Split override_dh_install into -arch and -indep -- Michael R. Crusoe Sat, 17 Feb 2018 09:22:51 -0800 seqan2 (2.4.0+dfsg-6) unstable; urgency=medium * Retry building on mips*; patch adapted from Adrian Bunk Closes: #890385. Thanks! * Document CWL generation via README.source. Mark all CWL files as executable * Enable AutoPackageTests for seqan-apps * Applied 2 patches from upstream: add mandatory ctdVersion element, fix errors in manpage output * Suggest cwltool | cwl-runner. -- Michael R. Crusoe Sat, 17 Feb 2018 07:09:41 -0800 seqan2 (2.4.0+dfsg-5) unstable; urgency=medium * Ship CWL descriptions for a subset of seqan-apps * Give up on mips & mipsel due to lack of memory -- Michael R. Crusoe Sun, 11 Feb 2018 01:54:55 -0800 seqan2 (2.4.0+dfsg-4) unstable; urgency=medium * Update seqan-config.cmake installation location as per upstream: https://github.com/seqan/seqan/issues/2276 * Drop mips* to -O2 from -O3 -- Michael R. Crusoe Fri, 09 Feb 2018 03:53:49 -0800 seqan2 (2.4.0+dfsg-3) unstable; urgency=medium * Remove parallel building form mips{,el} * AMD64 is freezing up on the builders, drop max parallel builds to 2 -- Michael R. Crusoe Thu, 08 Feb 2018 03:56:41 -0800 seqan2 (2.4.0+dfsg-2) unstable; urgency=medium * Drop mips{,el} down to 2 max parallel builds. * Latest release fixes the failing tests issue. (Closes: #884548) -- Michael R. Crusoe Wed, 07 Feb 2018 03:22:48 -0800 seqan2 (2.4.0+dfsg-1) unstable; urgency=medium * 2.4.0 is released! * Install seqan-2.pc to /usr/share/pkgconfig as it is arch independent -- Michael R. Crusoe Mon, 05 Feb 2018 07:52:07 -0800 seqan2 (2.4.0~rc2+dfsg-1) experimental; urgency=medium * Testing upstream's 3rd formal release candidate for 2.4.0 * debian/rules: use --max-parallel to more cleanly limit parallel building -- Michael R. Crusoe Wed, 31 Jan 2018 22:23:03 -0800 seqan2 (2.4.0~rc1+dfsg-2) experimental; urgency=medium * debian/rules: Drop amd64, mips, mipsel to -j3 to save memory -- Michael R. Crusoe Wed, 31 Jan 2018 04:16:59 -0800 seqan2 (2.4.0~rc1+dfsg-1) experimental; urgency=medium * Testing upstream's 2nd formal release candidate for 2.4.0 -- Michael R. Crusoe Tue, 30 Jan 2018 03:00:53 -0800 seqan2 (2.4.0~rc0+dfsg-1) experimental; urgency=medium * Testing upstream's formal release candidate -- Michael R. Crusoe Fri, 26 Jan 2018 10:14:15 -0800 seqan2 (2.3.2.001platform-issues10-6f85721+dfsg-2) experimental; urgency=medium * enable asyncio on all archs as a test * disable parallel building on powerpcspe -- Michael R. Crusoe Thu, 04 Jan 2018 05:11:43 -0800 seqan2 (2.3.2.001platform-issues10-6f85721+dfsg-1) experimental; urgency=medium * Hopefully final update from upstream :-) -- Michael R. Crusoe Wed, 03 Jan 2018 09:27:33 -0800 seqan2 (2.3.2.000platform-issues9-028fd79+dfsg-1) experimental; urgency=medium * Another update from upstream * debian/rules: build flags simplification: - use DEB_*_MAINT_APPEND - pass -DNDEBUG -O3 as per upstream - drop -DSEQAN_BUILD_SYSTEM=DEVELOP as that is the default -- Michael R. Crusoe Fri, 22 Dec 2017 00:03:51 -0800 seqan2 (2.3.2.000platform-issues8-6f85721+dfsg-2) experimental; urgency=medium * Force rebuild -- Michael R. Crusoe Thu, 14 Dec 2017 01:51:28 -0800 seqan2 (2.3.2.000platform-issues8-6f85721+dfsg-1) experimental; urgency=medium * Another update from upstream -- Michael R. Crusoe Fri, 08 Dec 2017 04:41:18 -0800 seqan2 (2.3.2.000platform-issues7-41f58c3+dfsg-2) experimental; urgency=medium [ Andreas Tille ] * Work around missing dir in indep-only builds Closes: #882169 [ Michael R. Crusoe ] * Cleanup from not pushing my changes -- Michael R. Crusoe Wed, 06 Dec 2017 05:28:59 -0800 seqan2 (2.3.2.000platform-issues7-41f58c3+dfsg-1) experimental; urgency=medium * Another update from upstream -- Michael R. Crusoe Tue, 21 Nov 2017 22:19:27 -0800 seqan2 (2.3.2.000platform-issues6-9cf5a69+dfsg-3) experimental; urgency=medium * Typo fix -- Michael R. Crusoe Sat, 18 Nov 2017 06:19:44 -0800 seqan2 (2.3.2.000platform-issues6-9cf5a69+dfsg-2) experimental; urgency=medium * Now try -O3 everywhere * Remove the sparc64 test code * Delete symlinks for apps that are skipped for a particular architecture -- Michael R. Crusoe Sat, 18 Nov 2017 04:50:55 -0800 seqan2 (2.3.2.000platform-issues6-9cf5a69+dfsg-1) experimental; urgency=medium * Skip yara on kfreebsd-i386 * Try out -O2 on archs that had been previously -O1 * Fix typo in bam2roi help text * From upstream: another round of changes for the problems that affect all big endian. -- Michael R. Crusoe Sat, 11 Nov 2017 05:44:36 -0800 seqan2 (2.3.2.000platform-issues5-86390dc+dfsg-1) experimental; urgency=medium * Another update from upstream including a tweak to sparc64 -- Michael R. Crusoe Wed, 08 Nov 2017 07:03:25 -0800 seqan2 (2.3.2.000platform-issues4-fba8744+dfsg-1) experimental; urgency=medium * Another refresh from upstream's branch * Skip yara on armel, as well. * d/control: declare seqan2 can be built without root, R³:no. -- Michael R. Crusoe Mon, 06 Nov 2017 12:15:11 -0800 seqan2 (2.3.2.000platform-issues3-1d438c8+dfsg-2) experimental; urgency=medium * Skip yara on armhf & sh4. * Disable parallel building on armel -- Michael R. Crusoe Sat, 04 Nov 2017 02:09:12 -0700 seqan2 (2.3.2.000platform-issues3-1d438c8+dfsg-1) experimental; urgency=medium * require tests to pass everywhere * skip the razers{3,} and yara apps on mips{el,} * restore parallel build blocking only for armhf, sh4, and kfreebsd* * Another refresh from upstream, this time focusing on bam files -- Michael R. Crusoe Thu, 02 Nov 2017 11:41:21 -0700 seqan2 (2.3.2.000platform-issues2-206d1f7+dfsg-1) experimental; urgency=medium * Typo for CXXFLAGS: -O1 instead of -01 * Another refresh from upstream in response to errors discovered via the Debian build machines. -- Michael R. Crusoe Thu, 26 Oct 2017 08:48:11 -0700 seqan2 (2.3.2.000platform-issues1-66a8baf+dfsg-1) experimental; urgency=medium * Refresh from upstream with additional fixes -- Michael R. Crusoe Wed, 25 Oct 2017 04:08:29 -0700 seqan2 (2.3.2.000platform-issues0-8ae7bc0+dfsg1-1) experimental; urgency=medium * Patch for mips64el from bunk@debian.org (Closes: #878933) * Temporarily enable all archs again * Upstream source is pre-2.4.0, remove patches that they have merged: short-description, spelling * Cleaned up per-arch settings in debian/rules -- Michael R. Crusoe Mon, 23 Oct 2017 09:58:43 -0700 seqan2 (2.3.2+dfsg2-4) unstable; urgency=medium * Work around missing dir in indep-only builds Closes: #882169 * d/rules: drop --parallel which is redundant for debhelper 10 * Do not generate manpages in arch indep builds (as done in experimental branch) -- Andreas Tille Wed, 06 Dec 2017 11:11:59 +0100 seqan2 (2.3.2+dfsg2-3) unstable; urgency=medium * Patch for mips64el from bunk@debian.org (Closes: #878933) * Cleaned up per-arch settings in debian/rules * Disable parallel building on sh4 -- Michael R. Crusoe Tue, 24 Oct 2017 04:56:12 -0700 seqan2 (2.3.2+dfsg2-2) unstable; urgency=medium * As per upstream, disable async-io for many platforms * Remove jinja2, python-nose, and dh-linktree dependencies as we are not yet building the docs * Switch to GitHub releases for HTTPS protection -- Michael R. Crusoe Fri, 13 Oct 2017 10:48:00 -0700 seqan2 (2.3.2+dfsg2-1) unstable; urgency=medium * Still not enough memory for seqan-apps on amrhf, disabling * seqan-apps: run tests post build, everywhere -- Michael R. Crusoe Fri, 13 Oct 2017 05:01:16 -0700 seqan2 (2.3.2+dfsg-2) unstable; urgency=medium * Re-enable armhf, h/t Ubuntu * Disabling armel again due to lack of memory on buildd. (Closes: #877349) -- Michael R. Crusoe Sat, 07 Oct 2017 10:28:57 -0700 seqan2 (2.3.2+dfsg-1) unstable; urgency=medium * New upstream release. * Re-enable armel, now that upstream bug fixed in https://gcc.gnu.org/bugzilla/show_bug.cgi?id=64735 * removed debian/patches/skip-SEQAN_PKGCFG_CFLAGS, incorporated upstream -- Michael R. Crusoe Thu, 28 Sep 2017 09:15:34 -0700 seqan2 (2.3.1+dfsg-5) unstable; urgency=medium * Team upload. * Make build reproducible. Thanks to Chris Lamb for the patch. Closes: #862484 -- Sascha Steinbiss Tue, 04 Jul 2017 23:24:52 +0200 seqan2 (2.3.1+dfsg-4) unstable; urgency=medium * Fix FTBFS when built with dpkg-buildpackage -A (thanks for the patch to Santiago Vila ) Closes: #864026 -- Andreas Tille Sat, 03 Jun 2017 16:15:29 +0200 seqan2 (2.3.1+dfsg-3.1) unstable; urgency=medium * Non-maintainer upload. * Fix broken /usr/bin/splazers symlink on 32-bit architectures. (Closes: #863669) -- Chris Lamb Mon, 29 May 2017 22:56:39 +0100 seqan2 (2.3.1+dfsg-3) unstable; urgency=medium * add patch FWDs, set HOME to fix manpages -- Michael R. Crusoe Sun, 15 Jan 2017 01:34:05 -0800 seqan2 (2.3.1+dfsg-2) unstable; urgency=medium * Remove archs with failing builds: armhf mips mipsel * Set SEQAN_REVISION to 'tarball' so that ccache isn't poisened by changes to debian/ * Release to unstable -- Michael R. Crusoe Sat, 14 Jan 2017 00:23:26 -0800 seqan2 (2.3.1+dfsg-1) experimental; urgency=medium * Try to save more memory on kfreebsd-* * Fix parallel build disabling to not produce warnings * New upstream release, three incorporated patched removed -- Michael R. Crusoe Fri, 13 Jan 2017 05:36:28 -0800 seqan2 (2.3.0~1.20161019~af07bc1+dfsg-4) experimental; urgency=medium * Try out -O3 for many architectures as that is upstream's default. * Skip unneeded build for -indep. * Fix architecture detection logic. * Fix from upstream for another sparc64 related typo. -- Michael R. Crusoe Wed, 26 Oct 2016 03:31:54 -0700 seqan2 (2.3.0~1.20161019~af07bc1+dfsg-3) experimental; urgency=medium * Fix recursive variable expansion error. -- Michael R. Crusoe Mon, 24 Oct 2016 07:54:44 -0700 seqan2 (2.3.0~1.20161019~af07bc1+dfsg-2) experimental; urgency=medium * Fix typo from upstream's patch. * Work around GNU Hurd TANDEM problem * Skip armel * Test -O1 for mips[el] * Test turning off parallel builds for armhf, mips, kfreebsd-* -- Michael R. Crusoe Thu, 20 Oct 2016 04:48:11 -0700 seqan2 (2.3.0~0.201610100~af07bc1+dfsg+1) experimental; urgency=medium * Second experimental build to test fix for #840030. Source from https://github.com/seqan/seqan/pull/1887/commits/af07bc19087e662117b70d733e963a1611aa9b9a -- Michael R. Crusoe Thu, 20 Oct 2016 02:06:15 -0700 seqan2 (2.3.0~0.20161011~73a5aaf+dfsg-1) experimental; urgency=low * Experimental build to test fix for #840030 -- Michael R. Crusoe Tue, 11 Oct 2016 07:08:05 -0700 seqan2 (2.2.0+dfsg-6) UNRELEASED; urgency=medium * Drop Soeren Sonnenburg from Uploaders -- Andreas Tille Sat, 03 Dec 2016 08:08:51 +0100 seqan2 (2.2.0+dfsg-5) unstable; urgency=medium * Fix build issue with boost 1.62 (Thanks for the patch to Graham Inggs ) Closes: #846617 * debhelper 10 * d/watch: version=4 -- Andreas Tille Fri, 02 Dec 2016 19:01:10 +0100 seqan2 (2.2.0+dfsg-4) unstable; urgency=medium * Restrict to known working archs for now. Closes: #840025 * Use upstream's patch. Closes: #840030, #840026 -- Michael R. Crusoe Tue, 11 Oct 2016 12:20:59 -0700 seqan2 (2.2.0+dfsg-3) unstable; urgency=medium * Fix arch specific build. Closes: #840023 * Remove shlibs:Depends from include-only library package * More spelling fixes * Fix manpage generation -- Michael R. Crusoe Sun, 09 Oct 2016 06:41:34 -0700 seqan2 (2.2.0+dfsg-2) unstable; urgency=medium * Team upload. * Declare Conflicts: with seqan-dev (API incompatible) See https://github.com/seqan/seqan/issues/1820 for upstream discussion. Closes: #838340. * Add CMake modules needed to build projects based on SeqAn. * Add pkg-config file. * Fix some typos in d/copyright. -- Sascha Steinbiss Sat, 24 Sep 2016 21:48:27 +0000 seqan2 (2.2.0+dfsg-1) unstable; urgency=medium * New upstream version * Separate packaging from legacy seqan * cme fix dpkg-control * moved debian/upstream to debian/upstream/metadata * disable doc creation which works differently than in previous versions * correct opts in d/watch * upgrade copyright * New Build-Depends: * python-jinja2 needed in test suite * libbz2-dev, python-sphinx, python-nose, default-jdk suggested by build system * d/copyright: Remove some minimised JS scripts without source which are packaged for Debian * seqan-dev.install: Fix location of include files, docs are somewhere else and should be moved to a separate package * New package seqan-doc * Moved to Git * Symlink to binaries only if these are part of the binary distribution -- Andreas Tille Fri, 12 Aug 2016 13:16:56 +0200