jellyfish (2.3.1-4) unstable; urgency=medium [ Michael R. Crusoe ] * d/patches/portability: forwarded upstream. [ Andreas Tille ] * Standards-Version: 4.7.0 (routine-update) * Disable i386 in Salsa CI -- Andreas Tille Mon, 09 Dec 2024 07:54:45 +0100 jellyfish (2.3.1-3) unstable; urgency=medium * Forwarded several patches upstream. * debian/patches/fix_catch.patch is no longer used, remove it. * Point to the Jellyfish 2.0 homepage * d/control: simplify architecture specifications by build-dep'ing on architecture-is-little-endian. * d/patches/drop_distutils: upgrade to setuptools. * d/control: s/pkg-config/pkgconf/g * d/control: stop building on 32-bit architectures, as per upstream's wishes: https://github.com/gmarcais/Jellyfish/pull/202#issuecomment- 2007544485 * d/control: undo the t64 migration, no longer needed. -- Michael R. Crusoe Tue, 19 Mar 2024 18:21:25 +0100 jellyfish (2.3.1-2.1) unstable; urgency=medium * Non-maintainer upload. * Rename libraries for 64-bit time_t transition. Closes: #1064157 -- Lukas Märdian Wed, 28 Feb 2024 13:23:36 +0000 jellyfish (2.3.1-2) unstable; urgency=medium [ Zhang Na ] * d/control: add loong64 support (Closes: #1059550) -- Étienne Mollier Mon, 01 Jan 2024 11:43:16 +0100 jellyfish (2.3.1-1) unstable; urgency=medium * New upstream version * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) * manpage_whatis_entry.patch: reduce. Most of the issues it addressed are now sorted, except the "\-" separating the whatis field. * reproducible.patch: remove: applied upstream. * fix_replacement_of_-L_option.patch: remove: applied upstream. * patch test_needs_bash: refresh. * fix-autoreconf.patch: delete: applied upstream. * gcc-12.patch: delete: applied upstream. -- Étienne Mollier Wed, 13 Dec 2023 18:21:15 +0100 jellyfish (2.3.0-17) unstable; urgency=medium * d/clean: new: cleanup build artifacts. (Closes: #1046793) * d/rules: cleanup dh_auto_clean override. This is made possible by the introduction of the d/clean file. * d/rules: remove config.h from header package. This fixes PACKAGE_NAME macro definition collision with potential autotools consumers in reverse dependencies, per lintian warning. * d/libjellyfish-2.0-2.lintian-overrides: fix broken override. * d/libjellyfish-2.0-2.lintian-overrides: remove unused override. * d/jellyfish-examples.lintian-overrides: renamed. The file is renamed to d/jellyfish.lintian-overrides. The content is also adjusted to reflect that the overriden spelling error moved package. -- Étienne Mollier Tue, 05 Dec 2023 19:11:55 +0100 jellyfish (2.3.0-16) unstable; urgency=medium [ Étienne Mollier ] * d/rules: output report when tests fail. [ Andreas Tille ] * Standards-Version: 4.6.2 (routine-update) * Rebuild using gcc-13 Closes: #1037702 -- Andreas Tille Sat, 15 Jul 2023 15:11:33 +0200 jellyfish (2.3.0-15) unstable; urgency=medium * Fix dh_missing Closes: #1017261 -- Andreas Tille Wed, 28 Sep 2022 21:48:56 +0200 jellyfish (2.3.0-14) unstable; urgency=medium * Add gcc-12.patch: fix ftbfs with gcc-12. Thanks to Guillaume Marçais (Closes: #1012953) * d/copyright: identify randomc.h is under GPL-3. * Standards-Version: 4.6.1 (routine-update) -- Étienne Mollier Wed, 22 Jun 2022 23:10:04 +0200 jellyfish (2.3.0-13) unstable; urgency=medium * Disable reprotest * Use python configuration from autoconf-archive Closes: #1009451 -- Andreas Tille Wed, 13 Apr 2022 09:28:09 +0200 jellyfish (2.3.0-12) unstable; urgency=medium * Do not hardcode Perl version Closes: #993326 -- Andreas Tille Tue, 31 Aug 2021 09:16:42 +0200 jellyfish (2.3.0-11) unstable; urgency=medium [ Andreas Tille ] * Fix Homepage Closes: #983273 [ Étienne Mollier ] * d/watch: repair broken link to github * add fix-autoreconf.patch; fix ftbfs with autoreconf 2.70 (Closes: #978843) * Standards-Version: 4.6.0 (routine-update) * Apply multi-arch hints. + libjellyfish-2.0-dev: Drop Multi-Arch: same. + jellyfish-examples: Add Multi-Arch: foreign. * d/control: add myself to uploaders -- Étienne Mollier Sat, 28 Aug 2021 21:01:20 +0200 jellyfish (2.3.0-10) unstable; urgency=medium [ Adrian Bunk ] * Also fix building with -l and -I in builddir in the existing -L fix Closes: #976340 -- Andreas Tille Tue, 02 Mar 2021 12:50:29 +0100 jellyfish (2.3.0-9) unstable; urgency=medium * Team upload. * Silence additional warning/error appearing with -O3. Closes: #973431 * Restrict to architectures that support the atomic instructions used by upstream. Closes: #976340 -- Sascha Steinbiss Sun, 21 Feb 2021 12:09:45 +0100 jellyfish (2.3.0-8) unstable; urgency=medium * Add Breaks+Replaces: jellyfish-examples (<< 2.3.0-7) Closes: #976429 -- Andreas Tille Sat, 05 Dec 2020 09:54:41 +0100 jellyfish (2.3.0-7) unstable; urgency=medium [ Michael R. Crusoe ] * For jellyfish-examples drop 'jellyfish' to a recommends from a depends. [ Nilesh Patra ] * Enable build on 32bit architectures Closes: #962184 [ Andreas Tille ] * Ignore tests on 32 bit architectures since test data are to big * Move some arch dependant binaries from examples to jellyfish package * Enable dh_missing --fail-missing * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) -- Andreas Tille Thu, 03 Dec 2020 14:13:45 +0100 jellyfish (2.3.0-6) unstable; urgency=medium [ Andreas Tille ] * Fix permission of shared library Closes: #962183 -- Michael R. Crusoe Thu, 04 Jun 2020 16:23:12 +0200 jellyfish (2.3.0-5) unstable; urgency=medium [ Andreas Tille ] * Architecture: any (for examples: all) * Standards-Version: 4.5.0 (routine-update) * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. -- Michael R. Crusoe Wed, 03 Jun 2020 21:04:40 +0200 jellyfish (2.3.0-4) unstable; urgency=medium * Remove NEWS.Debian now that we ship the python module again. * Force the use of Bash for testing -- Michael R. Crusoe Mon, 16 Dec 2019 16:19:39 +0100 jellyfish (2.3.0-3) unstable; urgency=medium * Upstream only supports AMD64 (Closes: #941920) * Use secure URI in Homepage field. * Set upstream metadata fields: Repository. -- Michael R. Crusoe Sun, 17 Nov 2019 14:23:43 +0100 jellyfish (2.3.0-2) unstable; urgency=medium * Restore jellyfish-examples, needed for the autopkgtest (Closes: #941262) * Enable an additional two test categories in the autopkgtests * Enabled htslib, to read SAM/BAM/CRAM files * Restore python3-dna-jellyfish package -- Michael R. Crusoe Fri, 27 Sep 2019 18:29:29 +0200 jellyfish (2.3.0-1) unstable; urgency=medium * Team upload [Andreas Tille] * Install config.h which is needed by sailfish package * New upstream version * debhelper-compat 12 [Steffen Moeller] * Standards-Version: 4.4.0 * d/u/metadata: Added ref to conda * deactivated installation of examples, which have changed considerably * removed build-dependency on python2 (prime reason to upload) -- Andreas Tille Thu, 01 Aug 2019 13:37:07 +0200 jellyfish (2.2.10-2) unstable; urgency=medium * debian/control: removed unused valgrind dependency * Standards-Version: 4.3.0 * Improve reproducibilty, drop /usr/share/doc/jellyfish- examples/examples/swig* * Remove dependency_libs field in libjellyfish-2.0.la. -- Michael R. Crusoe Mon, 24 Dec 2018 06:46:27 -0800 jellyfish (2.2.10-1) unstable; urgency=medium * New upstream version * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 * Adapt watch file to also catch v$VERSION tarball names * Clean up quilt patches * Catch exceptions by reference * Do not replace random '-L' strings in command line Closes: #907819 * Drop python3-dna-jellyfish package since the Python module had issues in build process and nobody seemed to be interested to help solving theses -- Andreas Tille Fri, 21 Sep 2018 08:45:53 +0200 jellyfish (2.2.8-3) unstable; urgency=medium * Build and install fastq2sam, which fixes Debci tests * Incorporates suggestions from the Multiarch hinter. -- Michael R. Crusoe Fri, 16 Mar 2018 10:57:09 -0700 jellyfish (2.2.8-2) unstable; urgency=medium * Add the missing small_mers.sh file, courtesy upstream. * Fix arm/powerpc build, patch courtesy upstream (Closes: #890137) -- Michael R. Crusoe Mon, 12 Mar 2018 05:31:00 -0700 jellyfish (2.2.8-1) unstable; urgency=medium * New upstream version * Dropped rename-python-module-to-dna_jellyfish.patch as upstream has incorporated it. -- Michael R. Crusoe Sun, 11 Feb 2018 09:21:51 -0800 jellyfish (2.2.7-1) unstable; urgency=medium * New upstream version * cme fix dpkg-control * debhelper 11 -- Andreas Tille Mon, 05 Feb 2018 22:22:17 +0100 jellyfish (2.2.6-6) unstable; urgency=medium * Really apply portability patch Closes: #871697 -- Andreas Tille Fri, 01 Sep 2017 12:42:21 +0200 jellyfish (2.2.6-5) unstable; urgency=medium * Make jellyfish portable (Thanks for the patch to Edmund Grimley Evans ) Closes: #871697 -- Andreas Tille Fri, 01 Sep 2017 00:09:35 +0200 jellyfish (2.2.6-4) unstable; urgency=medium * Make sure reproducible patch will not break test suite (Thanks to Chris Lamb for the fix) Closes: #863015 * Autoreconf not needed with debhelper 10 * Do not parse debian/changelog * Fix whatis entry in manpage * Fix spelling in manpage -- Andreas Tille Mon, 28 Aug 2017 14:40:40 +0200 jellyfish (2.2.6-3) unstable; urgency=medium * Explicitly disable parallel building Closes: #873318 -- Andreas Tille Sat, 26 Aug 2017 21:53:10 +0200 jellyfish (2.2.6-2) unstable; urgency=medium * Ignore result of "big" test to let autopkgtest pass * debhelper 10 * Parallel builds seem to cause problems - use --no-parallel * d/watch: version=4 * Do not fail on compiler warnings to enable building with gcc-7. (Thanks for the patch to Adrian Bunk ) Closes: #872262 * Enable full hardening Closes: #865608 * Standards-Version: 4.1.0 (no changes needed) -- Andreas Tille Fri, 25 Aug 2017 14:46:44 +0200 jellyfish (2.2.6-1) unstable; urgency=medium * New upstream version * Rename python module from python3-jellyfish to python3-dna-jellyfish (thanks for the patches to "Diego M. Rodriguez" ) Closes: #819016 * cme fix dpkg-control * hardening=+all,-pie -- Andreas Tille Tue, 30 Aug 2016 14:16:52 +0200 jellyfish (2.2.5-1) unstable; urgency=medium [ Andreas Tille ] * Enable Python and Perl bindings [ Scott Kitterman ] * Rename python-jellyfish to python3-jellyfish * Change python-dev build-dep to python3-all-dev (since this is a python3 extension) * Add dh-python to build-depends * Add building with python3 * Add call to setup.py in dh_autobuild override [ Michael R. Crusoe ] * New upstream version, fixes dataloss bug * Upgrade Standards-Version to 3.9.7 * Mark python3- package as arch specifc, not indep; include shared library dependencies * Likewise with the -perl package; also build & install them * debian/patches/drop-rpath: don't compile in a relative path as per policy * debian/patches/modern-g++: use recent g++, not the unavailable version 4.4 * debian/patches/pkg-config-with-name: fix error in upstream: pkg-config was called without the package name * debian/rules: enable parallel builds & improve clean target * debian/control: add myself as an uploader -- Michael R. Crusoe Sat, 12 Mar 2016 08:09:07 -0800 jellyfish (2.2.4-2) unstable; urgency=medium * enable build with c++11 and -Werror=deprecated-declarations compile flag (thanks for the hint to Gert Wollny) Closes: #808537 -- Andreas Tille Fri, 25 Dec 2015 12:17:44 +0100 jellyfish (2.2.4-1) unstable; urgency=medium * New upstream version -- Andreas Tille Tue, 10 Nov 2015 21:57:20 +0100 jellyfish (2.2.3-3) unstable; urgency=medium * team upload * include missing header -- Michael R. Crusoe Sun, 20 Sep 2015 08:46:24 +0200 jellyfish (2.2.3-2) unstable; urgency=medium [ Charles Plessy ] * Patch with Upstream commit a3c491a for GCC5; closes: #795847. [ Andreas Tille ] * Do not mention removed file from d/copyright -- Andreas Tille Thu, 20 Aug 2015 09:07:18 +0200 jellyfish (2.2.3-1) unstable; urgency=medium [ Andreas Tille ] * Replace unneeded dependency by @builddeps@ in debian/tests/control * New version needs valgrind as Build-Depends to pass all tests * New version closes: #777922 [ Charles Plessy ] * New upstream release. * Removed yaggo and clang patches, obsoleted upstream. -- Andreas Tille Fri, 03 Jul 2015 20:06:28 +0200 jellyfish (2.1.4-1) unstable; urgency=medium * New upstream version * d/watch: point to new location on Github * cme fix dpkg-control * new upstream version needs autoreconf * New Build-Depends: yaggo, pkg-config, bc, time, procps * debian/rules: Make sure package builds twice in a row * d/copyright: - Adapted to file locations in new upstream version - Additional copyright paragraph for included libjsoncpp - Additional copyright paragraph for unit tests * checking whether it is possible to use Debian packaged libjsoncpp failed - add lintian override to use internal one * Split libjellyfish and libjellyfish-dev packages up from single package, add jellyfish-examples package containing test suite * Add autopkgtest * Fix FTBFS with clang (thanks for the patch to Martin Steghöfer) Closes: #749136 -- Andreas Tille Thu, 09 Oct 2014 13:15:34 +0200 jellyfish (1.1.11-1) unstable; urgency=medium * New upstream version * Move debian/upstream to debian/upstream/metadata * cme fix dpkg-control -- Andreas Tille Fri, 21 Mar 2014 11:31:00 +0100 jellyfish (1.1.10-1) unstable; urgency=low * New upstream version Closes: #701423 * debian/{rules,install}: Make sure dynamic library will be installed * debian/control: - Removed DM-Upload-Allowed - Standards-Version: 3.9.4 (no changes needed) - Build-Depends autotools-dev - canonical VCS URLs * debian/lintian-overrides: Upstream decided to use a dynamic library without really intending to make this a development package * debian/doc-base: docbase control file * debian/patches/man: refreshed + DEP3 description -- Andreas Tille Wed, 05 Jun 2013 11:58:53 +0200 jellyfish (1.1.5-1) unstable; urgency=low * New upstream version fixing the FTBFS with gcc-4.7 bug Closes: #667214 * debian/patches/fix-unused-but-set-variable.patch: Removed because applied upstream -- Andreas Tille Mon, 21 May 2012 21:56:38 +0200 jellyfish (1.1.4-1) unstable; urgency=low * New upstream version * debian/patches/ptrdiff_t: Removed because applied upstream * debian/patches/cmdline: Removed because upstream code was changed in a way that it becomes superfluous * debian/patches/fix-unused-but-set-variable.patch: Due to the use of hardening flags warnings about unused-but-set-variable becomes an error - start working on a patch * debian/source/local-options: Add dpkg-source local-options hints * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Move citation from long desciption to debian/upstream - debhelper (>= 9) * debian/upstream: Use the agreed way to specify citations * debian/copyright: DEP5 verified using cme fix dpkg-copyright * debian/compat: 9 -- Andreas Tille Sat, 31 Mar 2012 08:50:25 +0200 jellyfish (1.1.2-1) unstable; urgency=low * Initial release. Closes: #644925. -- Shaun Jackman Mon, 10 Oct 2011 11:49:11 -0700