bowtie2 (2.3.0-2~bpo8+1) jessie-backports; urgency=medium * Rebuild for jessie-backports. -- Andreas Tille Tue, 06 Jun 2017 15:30:29 +0200 bowtie2 (2.3.0-2) unstable; urgency=medium * Team upload. [ Sascha Steinbiss ] * Skip tests involving simulated reads to avoid use of non-free build-dep libmath-random-perl again. Closes: #852546 * Add libclone-perl build dependency. [ Alexandre Mestiashvili ] * Add patch suppressing -Wmisleading-indentation warnings. [ Steffen Moeller ] * Adjust EDAM annotations. -- Sascha Steinbiss Wed, 25 Jan 2017 16:27:13 +0100 bowtie2 (2.3.0-1) unstable; urgency=medium * Team upload. [ Andreas Tille ] * New upstream version * Code available on Github * debhelper 10 * Remove Carlos Borroto from Uploaders * Remove code from test suite that is requiring non-free package libmath-random-perl * New Build-Depends to run build time test: liblocal-lib-perl [ Sascha Steinbiss ] * Even more new Build-Depends: libmath-random-perl, libtest-deep-perl * Disable rebuilding during tests -- Sascha Steinbiss Sat, 14 Jan 2017 07:50:51 +0000 bowtie2 (2.2.9-4) unstable; urgency=medium * Team upload. * Make build reproducible by adding compiler flags setting -fdebug-prefix-map. -- Sascha Steinbiss Thu, 25 Aug 2016 12:47:33 +0000 bowtie2 (2.2.9-3) unstable; urgency=medium * Team upload. * Fix building with GCC 6. Closes: #831157. -- Sascha Steinbiss Sat, 16 Jul 2016 03:22:51 +0000 bowtie2 (2.2.9-2) unstable; urgency=medium * Team upload. * Make build reproducible. - Remove embedding of build hostname, time and compiler. - Fix help2man wrapper heredoc. - Sort wildcard expansions in Makefile. - Pin down language settings. -- Sascha Steinbiss Sat, 21 May 2016 17:18:25 +0000 bowtie2 (2.2.9-1) unstable; urgency=medium * Imported Upstream version 2.2.9 * Bump Standards-Version * Revert the commit with applied patch * Update hardening.patch * Cleanup d/rules, remove CPPFLAGS as they are imported anyway -- Alexandre Mestiashvili Thu, 28 Apr 2016 09:26:48 +0200 bowtie2 (2.2.8-1~bpo8+1) jessie-backports; urgency=medium * Rebuild for jessie-backports. -- Andreas Tille Tue, 22 Mar 2016 09:30:26 +0100 bowtie2 (2.2.8-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version repackaged as xz * cme fix dpkg-control [ Alexandre Mestiashvili ] * Imported Upstream version 2.2.8 * d/rules: export DEB_BUILD_MAINT_OPTIONS = hardening=+all * d/copyright: Merge Files: stanzas and update years -- Alexandre Mestiashvili Sat, 12 Mar 2016 15:57:34 +0100 bowtie2 (2.2.6-2) unstable; urgency=medium [ Charles Plessy ] * d/rules: quote variables contents passed to Makefile, closes: #809076. -- Andreas Tille Mon, 28 Dec 2015 08:23:51 +0100 bowtie2 (2.2.6-1) unstable; urgency=medium * Imported Upstream version 2.2.6 * d/rules: WITH_TBB=1 -- Alexandre Mestiashvili Fri, 28 Aug 2015 09:31:45 +0200 bowtie2 (2.2.5-2) unstable; urgency=medium * Upload to unstable -- Alexandre Mestiashvili Tue, 28 Apr 2015 18:06:34 +0200 bowtie2 (2.2.5-1) experimental; urgency=medium * Imported Upstream version 2.2.5 -- Alexandre Mestiashvili Wed, 18 Mar 2015 10:09:35 +0100 bowtie2 (2.2.4-2) unstable; urgency=medium * d/control: add python dependency, needed to build bowtie2-build man page Closes: #769934 * d/watch: fix upstream url parsing, see #766878 * d/rules: remove byte-compiled bowtie2-buildc -- Alexandre Mestiashvili Tue, 18 Nov 2014 23:28:33 +0100 bowtie2 (2.2.4-1) unstable; urgency=medium [ Andreas Tille ] * d/control: Priority: optional * add missing DEP3 description [ Alexandre Mestiashvili ] * d/test/binary-run: test that binary work * d/test/control: add binary-run [ Andreas Tille ] * New upstream version * do uscan call directly in debian/rules instead of separate script * cme fix dpkg-control -- Andreas Tille Sun, 26 Oct 2014 07:08:46 +0100 bowtie2 (2.2.3-1) unstable; urgency=medium * Imported Upstream version 2.2.3 -- Alexandre Mestiashvili Tue, 03 Jun 2014 16:13:47 +0200 bowtie2 (2.2.2-1) unstable; urgency=medium * Imported Upstream version 2.2.2 -- Alexandre Mestiashvili Tue, 15 Apr 2014 13:40:01 +0200 bowtie2 (2.2.1-1) unstable; urgency=medium * Imported Upstream version 2.2.1 * d/changelog: updated Copyright years -- Alexandre Mestiashvili Fri, 07 Mar 2014 09:37:13 +0100 bowtie2 (2.2.0-1) unstable; urgency=medium [ Alexandre Mestiashvili ] * Imported Upstream version 2.2.0 [ James McCoy ] * Move debian/upstream to debian/upstream/metadata [ Alexandre Mestiashvili ] * refreshed patches, dropped fix_makefile_machine_detection.patch * d/control: bump Standards-Version Architecture: amd64 kfreebsd-amd64, starting from this version bowtie2 works on amd64 only added python to Depends: * d/rules: remove i386 related fixes,rules for new binaries * d/bowtie2.install: added new binaries introduced by the new version -- Alexandre Mestiashvili Thu, 20 Feb 2014 13:29:58 +0100 bowtie2 (2.1.0-2) unstable; urgency=low * Closes: #713000 * d/control: fixed description for bowtie2-examples, bumped Standards-Version, removed DM-Upload-Allowed, use canonical vcs * d/tests/: underscore are not allowed for tests -- Alexandre Mestiashvili Tue, 25 Jun 2013 13:58:18 +0200 bowtie2 (2.1.0-1) unstable; urgency=low * - d/help2man-wrapper: as kindly suggested by Andreas Tille Closes: #701686 - d/rules: use help2man-wrapper instead of help2man to generate man pages * Imported Upstream version 2.1.0 * refreshed patches -- Alexandre Mestiashvili Wed, 27 Feb 2013 15:58:40 +0100 bowtie2 (2.0.6-1) unstable; urgency=low * Imported Upstream version 2.0.6 -- Alexandre Mestiashvili Tue, 19 Feb 2013 17:30:42 +0100 bowtie2 (2.0.5-1) unstable; urgency=low * Imported Upstream version 2.0.5 -- Alexandre Mestiashvili Fri, 11 Jan 2013 11:19:34 +0100 bowtie2 (2.0.4-1) unstable; urgency=low * Imported Upstream version 2.0.4 -- Alexandre Mestiashvili Thu, 27 Dec 2012 17:33:36 +0100 bowtie2 (2.0.2-1) unstable; urgency=low [ Carlos Borroto ] * Imported Upstream version 2.0.2 * bowtie2_gcc4.7.patch no longer needed [ Alexandre Mestiashvili ] * added autopkgtest testsuite * updated Uploaders field -- Alexandre Mestiashvili Mon, 19 Nov 2012 16:31:02 +0100 bowtie2 (2.0.0-beta7-1) unstable; urgency=low [ Alexandre Mestiashvili ] * debian/control force architcures to i386/amd64 kfreebsd-i386/amd64 and hurd-i386 SSE is not availbale on others. Closes: #668123 * debhelper version 9 * debian/rules forced hardening flags * hardening.patch to inject hardening CPPFLAGS * Imported Upstream version 2.0.0-beta7 * debian/bowtie2.lintian-overrides to avoid lintian's waring to be fixed by using epochs and tilda in upstream version -- Alexandre Mestiashvili Mon, 30 Jul 2012 13:51:31 +0200 bowtie2 (2.0.0-beta6-3) unstable; urgency=low * normalized architecture detection. For example kfreebsd-amd64 is detected as an amd64 architecture and msse flag is set.(Previous commit was wrong) (Closes: #673159) -- Alexandre Mestiashvili Fri, 01 Jun 2012 21:58:49 +0200 bowtie2 (2.0.0-beta6-2) unstable; urgency=low * debian/rules normalized output of dpkg-architecture, so for example kfreebsd-amd64 is detected as an amd64 architecture and sse flags are enabled for it. -- Alexandre Mestiashvili Thu, 31 May 2012 19:22:56 +0200 bowtie2 (2.0.0-beta6-1) unstable; urgency=low * updated debian/watch and get-orig-source to track -source suffix * Imported Upstream version 2.0.0-beta6 * debian/patches/fix_makefile_machine_detection.patch use -msse2 only for Intel architectures, Closes: #672526 -- Alexandre Mestiashvili Fri, 11 May 2012 08:41:59 +0200 bowtie2 (2.0.0-beta5-2) unstable; urgency=low [ Alexandre Mestiashvili ] * file sse_util.h has missing copyright header. The Author (Benjamin Langmead) has confirmed that the file is distributed under GPL3 license. [ Andreas Tille ] * debian/upstream: Added publication * debian/patches/fix_makefile_machine_detection.patch + debian/rules: prevent -mXX and -msse2 switches for non Intel architectures [ Alexandre Mestiashvili ] * debian/patches/bowtie2_gcc4.7.patch Closes: #672090 * updated DEP3 headers * bumperd Standards-Version to 3.9.3 * uname -m doesn't detect 32 bit chroot env - updated patcH -- Andreas Tille Thu, 26 Apr 2012 13:59:54 +0200 bowtie2 (2.0.0-beta5-1) unstable; urgency=low [ Alexandre Mestiashvili ] * Initial release (Closes: #660762) -- Alexandre Mestiashvili Wed, 22 Feb 2012 11:03:03 +0100