subread (2.0.7+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version 2.0.7+dfsg * typo.patch: refresh. * arch_specific_flags.patch: refresh. * d/control: declare compliance to standards version 4.7.0. -- Étienne Mollier Sat, 31 Aug 2024 11:09:35 +0200 subread (2.0.6+dfsg-3) unstable; urgency=medium * Team upload. * d/control: simplify architecture specification by using the provisions from the architecture-properties package. * d/rules: preserve original mm39_RefSeq_exon.txt.gz to enable building twice. Closes: #1049300 * d/control: update description of subread-data to include the gene annotations for both the hh39 and mm39 genomes. * d/patches/arch_specific_flags.patch: since -D_FILE_OFFSET_BITS=64 is set, use fopen() even on 32-bit systems. Closes: #1069030 Thanks to blhc "E-pointer-trouble-at-implicit" for pointing this out. * d/patches/cross.patch: deleted, as it was unused and incorporated into arch_specific_flags.patch by Alexandre Mestiashvili. * d/upstream/metadata: add publications, bug info, changelog, link to user guide PDF. * d/test/control: python3 is needed -- Michael R. Crusoe Thu, 25 Apr 2024 13:38:39 +0300 subread (2.0.6+dfsg-2) unstable; urgency=medium * Team upload. * d/control: build on riscv64 as well. * d/patches/0001-src-Makefile.Linux-Do-not-set-CFLAGS-and-CXXFLAGS- to.patch: fix embedded build path in various binaries. Thanks to Vagrant Cascadian . Closes: #1033089. -- Michael R. Crusoe Wed, 13 Sep 2023 14:21:47 +0200 subread (2.0.6+dfsg-1) unstable; urgency=medium * New upstream version * Add loong64 to list of architectures Closes: #1050423 -- Andreas Tille Fri, 25 Aug 2023 09:19:12 +0200 subread (2.0.4+dfsg-1) unstable; urgency=medium [ Nilesh Patra ] * [skip ci] Remove myself from uploaders [ Alexandre Mestiashvili ] * d/copyright, remove .o files and prebuilt binary from src/longread-one * New upstream version 2.0.4+dfsg * d/patches, update and refresh, incorporare cross.patch into arch_specific_flags.patch * d/*.1, generate manpages * remove unused d/filter.pl * d/control: - debhelper-compat 13 - Policy version 4.6.2 -- Alexandre Mestiashvili Sat, 11 Mar 2023 12:49:17 +0100 subread (2.0.3+dfsg-1) unstable; urgency=medium * Annotate test-only B-D with * d/p/cross.patch: Fix non-cross buildability * d/rules: Remove hardcoding on make * Do not generate manpages during build time - Added createmanpages script which can be manually run at each release (Closes: #984978) * New upstream version 2.0.3+dfsg * Refresh patch, remove gcc10.patch * Declare compliance with policy 4.5.1 -- Nilesh Patra Sun, 15 Aug 2021 17:47:45 +0530 subread (2.0.1+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version * Standards-Version: 4.5.0 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Archive. (routine-update) * Rely on pre-initialized dpkg-architecture variables. (routine-update) * d/rules: extended clean to allow consecutive builds * d/copyright: excluded changing test/*gz files from source tree -- Steffen Moeller Fri, 22 May 2020 19:31:20 +0200 subread (2.0.0+dfsg-2) unstable; urgency=medium * Add patch to build with gcc-10 Closes: #957846 -- Nilesh Patra Sat, 18 Apr 2020 21:55:06 +0530 subread (2.0.0+dfsg-1) unstable; urgency=medium * New upstream version * Use 2to3 to port to Python3 Closes: #938576 -- Andreas Tille Thu, 05 Sep 2019 09:30:37 +0200 subread (1.6.5+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version * Standards-Version: 4.4.0 -- Steffen Moeller Fri, 09 Aug 2019 16:21:31 +0200 subread (1.6.4+dfsg-1) unstable; urgency=medium * Update d/watch, add uversionmangle to remove -source suffix * New upstream version 1.6.4+dfsg * Refresh patches, update typo.patch * Switch to debhelper-compat, drop d/compat * Install genRandomReads binary and generate man page -- Alexandre Mestiashvili Tue, 30 Apr 2019 10:58:08 +0200 subread (1.6.3+dfsg-1) unstable; urgency=medium [ Alexandre Mestiashvili ] * New upstream version 1.6.3+dfsg * DH_VERBOSE=1, check for nocheck in DEB_BUILD_OPTIONS * Bump Policy to 4.3.0 * Refresh patches * Don't install buggy detectionCall binary * Update d/README.Debian [ Andreas Tille ] * debhelper 12 -- Alexandre Mestiashvili Wed, 30 Jan 2019 20:19:47 +0100 subread (1.6.2+dfsg-1) unstable; urgency=medium * New upstream version 1.6.2+dfsg * d/control: - bump Policy to 4.1.4 - update uploader's email in d/{control,copyright} - bump compat to 11 * Remove --parallel from dh invocation in d/rules * Generate man page for flattenGTF with help2man * Install new binary flattenGTF * Refresh and update patches -- Alexandre Mestiashvili Fri, 18 May 2018 19:07:58 +0200 subread (1.6.1+dfsg-1) unstable; urgency=medium [ Steffen Möller ] * Added new d/u/metadata file [ Alexandre Mestiashvili ] * New upstream version 1.6.1+dfsg * Update d/control, bump Policy to 4.1.3, fix Vcs-* fields to point to salsa * Refresh patches * Update copyright years -- Alexandre Mestiashvili Wed, 04 Apr 2018 17:04:57 +0000 subread (1.6.0+dfsg-1) unstable; urgency=medium * Update d/watch to version 4 * New upstream version 1.6.0+dfsg * Update d/subread.install, add sublong and txUnique binaries * d/rules: - add man page generation for sublong binary - use conditional variable assignment operator for DEB_HOST_ARCH * d/control: - bump Standards-Version to 4.1.1 - drop autopkgtest testsuite from d/control as we have d/tests/control * Update arch_specific_flags patch, fix Makefile for sublong -- Alexandre Mestiashvili Fri, 17 Nov 2017 16:43:55 +0100 subread (1.5.3+dfsg-1) unstable; urgency=medium * Bump Standards-Version to 4.0.0 * New upstream version 1.5.3+dfsg * Refresh and update paches * Update man pages * Remove trailing whitespaces from changelog -- Alexandre Mestiashvili Fri, 28 Jul 2017 16:09:49 +0200 subread (1.5.2+dfsg-1) unstable; urgency=medium * New upstream version 1.5.2+dfsg * Refresh and update patches * Add d/patches/typo.patch fixing a typo in featureCounts -- Alexandre Mestiashvili Tue, 21 Mar 2017 16:18:52 +0100 subread (1.5.1+dfsg-4) unstable; urgency=medium * Fix watch file * debhelper 10 * remove outdated information from README.source -- Andreas Tille Fri, 02 Dec 2016 08:22:05 +0100 subread (1.5.1+dfsg-3) unstable; urgency=medium * Pass triplet-prefixed CC to make -- Alexandre Mestiashvili Mon, 05 Sep 2016 14:59:37 +0200 subread (1.5.1+dfsg-2) unstable; urgency=medium * Team upload. * Make build reproducible. - Add compiler flags to ensure use of -fdebug-prefix-map. -- Sascha Steinbiss Sun, 04 Sep 2016 15:16:33 +0000 subread (1.5.1+dfsg-1) unstable; urgency=medium * Imported Upstream version 1.5.1+dfsg * Fix copyright Format: s/http/https/ * Refresh and remove applied patches -- Alexandre Mestiashvili Sun, 28 Aug 2016 08:43:33 +0200 subread (1.5.0-p3+dfsg-3) unstable; urgency=medium * Team upload. * Further address reproducibility by forcing mode on tarball contents. -- Sascha Steinbiss Thu, 21 Jul 2016 13:23:14 +0000 subread (1.5.0-p3+dfsg-2) unstable; urgency=medium * Team upload. * Make build reproducible by ensuring umask and mtime of archive contents are deterministic. -- Sascha Steinbiss Mon, 18 Jul 2016 07:46:12 +0000 subread (1.5.0-p3+dfsg-1) unstable; urgency=medium * Drop get-orig-source target, update d/watch to repack and use compression xz * Imported Upstream version 1.5.0-p3+dfsg -- Alexandre Mestiashvili Sat, 04 Jun 2016 09:16:27 +0200 subread (1.5.0-p2+dfsg-3) unstable; urgency=medium * Fix build on armel, armhf, arm64 and ppc64el It appears that -fsigned-char option must be defined before other CFLAGS or some binaries fail to work on architectures defined above -- Alexandre Mestiashvili Tue, 26 Apr 2016 22:44:51 +0200 subread (1.5.0-p2+dfsg-2) unstable; urgency=medium * Cleanup d/rules * Add patch fixing ftbfs on kfreebsd -- Alexandre Mestiashvili Sat, 23 Apr 2016 22:19:34 +0200 subread (1.5.0-p2+dfsg-1) unstable; urgency=medium * Imported Upstream version 1.5.0-p2+dfsg * Refresh patches * Add --parallel to dh $@ * Update arch_specific_flags.patch: append CFLAGS and LDFLAGS instead of hardcoding them in the Makefile * Cme fix dpkg, update VCS fields, bump Standards-Version * Add python and bc to Build-Depends, needed for tests * Run all tests -- Alexandre Mestiashvili Fri, 22 Apr 2016 18:09:24 +0200 subread (1.5.0-p1+dfsg-2) unstable; urgency=medium * d/control: remove hurd-i386 and mipsel due to failing tests -- Alexandre Mestiashvili Mon, 18 Jan 2016 12:03:41 +0100 subread (1.5.0-p1+dfsg-1) unstable; urgency=medium * Imported Upstream version 1.5.0-p1+dfsg * d/patches: refresh and remove applied patches -- Alexandre Mestiashvili Tue, 05 Jan 2016 15:58:47 +0100 subread (1.5.0+dfsg-1) unstable; urgency=medium * Imported Upstream version 1.5.0+dfsg * no PDF documentation in this release * removed globalReassembly and subtools binaries, added "repair" tool -- Alexandre Mestiashvili Fri, 06 Nov 2015 15:05:00 +0100 subread (1.4.6-p5+dfsg-1) unstable; urgency=medium * Imported Upstream version 1.4.6-p5+dfsg * Build and install SubreadUsersGuide.pdf -- Alexandre Mestiashvili Sat, 05 Sep 2015 12:35:30 +0200 subread (1.4.6-p4+dfsg-1) unstable; urgency=medium * d/patches/arch_specific_flags.patch: set the optimization level to -03 because -O levels higher than 3 have no effect. * Imported Upstream version 1.4.6-p4+dfsg -- Alexandre Mestiashvili Mon, 06 Jul 2015 15:51:55 +0200 subread (1.4.6-p3+dfsg-2) unstable; urgency=medium * d/changelog: upload to unstable, forgot to include the amd64 architecture in d/contorl * d/control: added amd64 to Architecture -- Alexandre Mestiashvili Thu, 21 May 2015 20:56:14 +0200 subread (1.4.6-p3+dfsg-1) unstable; urgency=medium * d/changelog: upload to unstable * d/rules: enable -fsigned-char for all architectures * d/patches/arch_specific_flags.patch: use -O2 instead of -O9 * d/control: not building for powerpc, mips, s390x, see d/README.source * d/README.source: merge with d/README.Debian-source describe the reason for not building on some architectures * Imported Upstream version 1.4.6-p3+dfsg -- Alexandre Mestiashvili Tue, 19 May 2015 13:51:49 +0200 subread (1.4.6-p2+dfsg-4) experimental; urgency=medium * d/rules: add -msse3 and -mtune=generic for i386/amd64 * d/patches: merge hardening and gcc_flags_cleanup patches * d/patches: updated and renamed getopt4exactSNP.patch to getopt.patch fixed 2 more issues with wrong assignment for the getopt_long function -- Alexandre Mestiashvili Mon, 18 May 2015 17:46:15 +0200 subread (1.4.6-p2+dfsg-3) experimental; urgency=medium * d/patches/getopt4exactSNP.patch: attempt to fix #784929 -- Alexandre Mestiashvili Wed, 13 May 2015 22:22:24 +0200 subread (1.4.6-p2+dfsg-2) unstable; urgency=medium * d/patches/gcc_flags_cleanup.patch: remove -mtune=core2 and mmmx,msse* flags Closes: #784780 * d/rules: use override_dh_installexamples-indep, Closes: #784782 * d/README.Debian-source: mention doc/SubreadUserGuide.pdf removal -- Alexandre Mestiashvili Sun, 10 May 2015 10:43:19 +0200 subread (1.4.6-p2+dfsg-1) unstable; urgency=medium * Actual first upload after fixing ftpmaster issues Closes: #779014 * d/copyright: exclude pdf without source files * d/patches: add Descriptions * d/watch: use repacksuffix to add +dfsg suffix * Imported Upstream version 1.4.6-p2+dfsg -- Alexandre Mestiashvili Thu, 07 May 2015 21:13:48 +0200 subread (1.4.6-p2-1) UNRELEASED; urgency=medium * Imported Upstream version 1.4.6-p2 * fixed regexps for man pages cleanup * d/README.Debian: add note about subread user guide url * d/doc-base: remove, as no documentation supplied with the package * d/subread.docs: remove SubreadUserGuide.pdf -- Alexandre Mestiashvili Thu, 23 Apr 2015 10:22:03 +0200 subread (1.4.6-p1-1) unstable; urgency=low * Initial release. Closes: #779014 -- Alexandre Mestiashvili Fri, 20 Feb 2015 10:48:06 +0100