bowtie (1.2.2+dfsg-2) unstable; urgency=medium * Update d/tests/run-unit-test - export BOWTIE_INDEXES, Closes: #888844 - enable test for example9 * Bump Standards-Version to 4.1.3 (No changes needed), set debhelper & d/compat to version 11 -- Alexandre Mestiashvili Wed, 31 Jan 2018 14:04:41 +0100 bowtie (1.2.2+dfsg-1) unstable; urgency=medium * New upstream version 1.2.2~beta+dfsg * Refresh patches * New upstream version 1.2.2+dfsg * Refresh patches * Bump Standards-Version to 4.1.2 * Update copyright, note license change to Artistic License 2.0 -- Alexandre Mestiashvili Sat, 16 Dec 2017 19:17:18 +0100 bowtie (1.2.1.1+dfsg-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version * Moved packaging from SVN to Git * debhelper 10 * Simplified d/watch * Build-Depends: zlib1g-dev [ Steffen Moeller ] * debian/upstream/metadata: - Completed references to registries - yamllint cleanliness [ Alexandre Mestiashvili ] * Update d/copyright: - use https for Format field - link to versioned license - add .cvsignore to Files-Excluded list - add myself to debian/* section * Add myself to uploaders, bump Standards-Version * Rearrange patch headers (cme fix dpkg), update spelling.patch * Re-introduce no_hash_style_both_for_mips.patch fixing build on mips64el Closes: #864448 * Update d/rules: - drop get-orig-source target - hardcode binary package name instead of using dpkg-parsechangelog * Disable unit tests for example6 and example9 as the output is different compared to older bowtie versions * Override lintian's warnings for binaries used with wrapper scripts -- Alexandre Mestiashvili Thu, 19 Oct 2017 20:35:11 +0200 bowtie (1.2.0+dfsg-1) unstable; urgency=medium * New upstream version. - Threading with tbb - queue-based lock rather than spin/heavyweight lock - reduced thread synchronization * Added 'dfsg' to version because of removed seqan source tree * debian/upstream/metadata: Added RRID reference * debian/watch: Adjusted for new distribution via github * Team upload provided by new aspiring Debian Med member, sponsored by -- Stephan Struckmann Thu, 08 Jun 2017 15:24:17 +0200 bowtie (1.1.2-6) unstable; urgency=medium * Enable build on all 64bit architectures (thanks for the patch to James Cowgill ) Closes: #840775 -- Andreas Tille Fri, 14 Oct 2016 20:53:17 +0200 bowtie (1.1.2-5) unstable; urgency=medium * Team upload. * Make build reproducible again. - Remove build directory from recorded CFLAGS. -- Sascha Steinbiss Wed, 07 Sep 2016 10:13:36 +0000 bowtie (1.1.2-4) unstable; urgency=medium * Team upload. * Make build reproducible. - Use fixed build hostname and compiler version. * Fix autopkgtest by adjusting directory. * Enable full hardening. * Bump Standards-Version. * Use secure Vcs-Browser. -- Sascha Steinbiss Wed, 25 May 2016 22:25:27 +0000 bowtie (1.1.2-3) unstable; urgency=medium * Enable building arch independent packages separately Closes: #806220 * Fix clean target -- Andreas Tille Wed, 25 Nov 2015 22:38:02 +0100 bowtie (1.1.2-2) unstable; urgency=medium * Enable building on arm64 (Thanks for the patch to Edmund Grimley Evans) Closes: #800548 * Remove inactive Uploader * Fix spelling -- Andreas Tille Thu, 01 Oct 2015 09:47:23 +0200 bowtie (1.1.2-1) unstable; urgency=medium * New upstream version * remove strange byte-compyled Python code bowtie-buildc (no idea how and why it was created) * Enabling ppc64el on Makefile and debian/control (Thanks for the patch to Fernando Seiti Furusato ) Closes: #788537 -- Andreas Tille Sun, 05 Jul 2015 21:24:20 +0200 bowtie (1.1.1-2) unstable; urgency=high * Team upload. * Install missing commands. Closes: #776881. -- Charles Plessy Tue, 03 Feb 2015 10:44:39 +0900 bowtie (1.1.1-1) unstable; urgency=medium * New upstream release * cme fix dpkg-control * Another patch to build with SeqAn 1.4 (Thanks to Gert Wollny) * Add Depends: python (also Build-Depends since it is used in tests) -- Andreas Tille Thu, 02 Oct 2014 14:32:50 +0200 bowtie (1.0.1-3) unstable; urgency=medium * Drop all architectures except amd64 since there was no success in trying to port the code to other architectures. The portability patch introduced in the last revision was droped again * debian/copyright: Drop unneeded copyright statements about code that was removed from upstream source -- Andreas Tille Mon, 15 Sep 2014 11:00:25 +0200 bowtie (1.0.1-2) unstable; urgency=medium * Do not use copy of outdated gcc header file which destroys portability to other architectures Closes: #756780 * Add README.Debian informing users about the fact that we ignore copy of cpuid.h * Add unit tests for build time and autopkgtest * Add debian/README.test to explain how to test the package Attention: Please take notice of /usr/share/bowtie/README.Debian about "Test suite for bowtie created and potential issue with sorting" -- Andreas Tille Wed, 03 Sep 2014 09:50:22 +0200 bowtie (1.0.1-1) unstable; urgency=medium * New upstream version (adapted patches) * drop debian/get-orig-source but rather remove the SeqAn-1.1 code copy via Files-Excluded * debian/control: Priority: optional -- Andreas Tille Wed, 30 Jul 2014 13:38:25 +0200 bowtie (1.0.0-6) unstable; urgency=low * debian/patches/seqan-popcount.patch: New patch. (Closes: #733398) * Version 1.4 of seqan-dev is required now. * Standards-Version: 3.9.5 (no changes needed). * Updated Vcs-Svn and Vcs-Browse fields as per Debian-Med policy. -- Ognyan Kulev Sat, 08 Mar 2014 15:13:16 +0200 bowtie (1.0.0-5) unstable; urgency=low * Fixed (hopefully) FTBFS by using override_dh_fixperms-indep target instead of override_dh_fixperms in debian/rules. -- Ognyan Kulev Thu, 30 May 2013 09:41:25 +0300 bowtie (1.0.0-4) unstable; urgency=low * Lintian fixes: - Removed DM-Upload-Allowed field. - Standards Version 3.9.4 (no changes needed). - Remove execute bits on some files in bowtie-examples. * Don't compress *.ebwt index files in bowtie-examples package. * Package description now starts with a capital letter. -- Ognyan Kulev Wed, 29 May 2013 22:53:13 +0300 bowtie (1.0.0-3) unstable; urgency=low * New patch no_hash_style_both_for_mips.patch. This fixes build errors on mips and mipsel. -- Ognyan Kulev Wed, 24 Apr 2013 15:15:37 +0300 bowtie (1.0.0-2) unstable; urgency=low * Requires version 1.3 of SeqAn. * Updated README.source about using Debian's SeqAn library. * Removed machine_bits_detection.patch and added disable_bits_flag.patch. -- Ognyan Kulev Wed, 24 Apr 2013 10:49:47 +0300 bowtie (1.0.0-1) unstable; urgency=low * New upstream version. (Closes: #705616) * Refreshed patches: use_debian_seqan.patch, use-dpkg-buildflags.patch. * Removed patch gcc-4.7.patch (fixed upstream). * New patch machine_bits_detection.patch. * Added build dependancy on seqan-dev. * Activated use_debian_seqan.patch and added the following patches: - seqan-fix-setBegin-call.patch - seqan-rename-ChunkPool.patch - seqan-rename-fill-to-resize.patch * Added myself to Uploaders control field. -- Ognyan Kulev Tue, 23 Apr 2013 16:43:49 +0300 bowtie (0.12.7-3) unstable; urgency=low * debian/patches/use-dpkg-buildflags.patch: Regard LDFLAGS/CPPFLAGS hardening flags (thanks for the patch to Simon Ruderich ) Closes: #670230 -- Andreas Tille Tue, 24 Apr 2012 13:21:32 +0200 bowtie (0.12.7-2) unstable; urgency=low * Do not give a pointer to non existing info pages in manpages * debian/control: - fixed Vcs fields - Standards-Version: 3.9.3 (no changes needed) * debian/upstream: Add citation information * debian/rules: calculate pkg name instead of setting it * debian/copyright: DEP5 verified using cme fix dpkg-copyright * debian/patches/gcc-4.7.patch: function "reverseInPlace" is declared after the function is used Thanks to Rodolfo García Peñas and gregor herrmann Closes: #667120 * debhelper 9 (control+compat) Hardening flags were explicitly tested but not enforced in debian/rules -- Andreas Tille Sun, 22 Apr 2012 21:09:05 +0200 bowtie (0.12.7-1) unstable; urgency=low * Initial release (Closes: #604940) -- Andreas Tille Wed, 02 Feb 2011 13:47:12 +0100