sra-sdk (2.10.9+dfsg-2) unstable; urgency=medium * run-unit-test: Give up for now on {abi,fastq,illumina,sff}-load. All four rely deeply on retired VDB functionality that would be too awkward to reintroduce. * skip_broken_loaders.patch (new): Likewise stop building or trying to install anything from tools/sra-load, to avoid leading users on. -- Aaron M. Ucko Thu, 04 Feb 2021 20:38:51 -0500 sra-sdk (2.10.9+dfsg-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * d/watch: - file standard 4 - Use filemangle to make sure the archive will not mixed up with other ncbi code with same version * Remove default debian/gbp.conf * Bump versioned Build-Depends: libngs-sdk-dev (>= 2.10.9) * Drop patch reenable_legacy_schema_in_sra_load.patch -- Andreas Tille Mon, 18 Jan 2021 09:23:28 +0100 sra-sdk (2.10.7+dfsg-1) unstable; urgency=medium * New upstream version * Trim trailing whitespace. * Set field Upstream-Contact in debian/copyright. * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. * Remove obsolete field Contact from debian/upstream/metadata (already present in machine-readable debian/copyright). -- Aaron M. Ucko Tue, 02 Jun 2020 21:47:38 -0400 sra-sdk (2.10.6+dfsg-5) unstable; urgency=medium * debian/patches/reenable_legacy_schema_in_sra_load.patch: New patch to make use of ncbi-vdb's new SRAUseLegacyDefaultSchema toggle, unbreaking tools/sra-load (fastq-load et al.) (Closes: #961347.) * debian/control: Ensure that this toggle is available at build time and at runtime. -- Aaron M. Ucko Mon, 25 May 2020 22:45:07 -0400 sra-sdk (2.10.6+dfsg-4) unstable; urgency=medium * Account for new sratools setup. (Closes: #961256.) - debian/rules: Rework deversioning logic to account for sratools and *-orig.* while still keeping hardcoding to a minimum; formally supply a hardcoded but originally random standard installation ID in a new /etc/ncbi/debian.kfg. - debian/patches/use_unversioned_tools.patch (new): Have sratools look for executable names without version extensions. -- Aaron M. Ucko Fri, 22 May 2020 09:25:13 -0400 sra-sdk (2.10.6+dfsg-3) unstable; urgency=medium * Also exclude sra-pileup check_skiplist test per network access. -- Aaron M. Ucko Thu, 21 May 2020 10:17:04 -0400 sra-sdk (2.10.6+dfsg-2) unstable; urgency=medium * drop_tests.patch: Exclude kar (needs network access); retire test-vdb-config exclusion with (fake)root out of the picture. Update description accordingly. * ignore_failing_test_for_the_moment_FIXME.patch: Resync. -- Aaron M. Ucko Thu, 21 May 2020 09:03:42 -0400 sra-sdk (2.10.6+dfsg-1) unstable; urgency=medium [ Steffen Moeller ] * New upstream version * debhelper-compat 12 * Standards-Version: 4.4.1 * ncbi-vdb needs to appear as 2.10.2 in Debian with its mbedtls wrapper fixed to avoid a link error in this package. [ Michael R. Crusoe ] * Convert to Python3. Closes: #943231 * Standards-Version: 4.5.0 (routine-update) [ Aaron M. Ucko ] * Correct accidental cutover to ncbi-vdb 2.10.5(+dfsg); further update to 2.10.6. * Revert patch updates contingent on spurious cutover to ncbi-vdb. * Refresh patches for real. - Generally standardize on -pab format. - hardening.patch: Rebase C(P)FLAGS, which no longer request extensions. - python3: Drop makefile tweaks obsoleted by new PYTHON abstraction. * Help validate-names4.c find ncbi-vdb headers that are normally internal. To wit, build-depend on libncbi-vdb-dev (>= 2.10.6+dfsg-2~) to ensure these headers are installed sanely, and patch validate-names4.c accordingly in a new patch use_exposed_headers.patch. In conjunction with taking the latest upstream, closes: #961049. * Specify configuration location by passing KONFIG_DIR. (The makefile patch previously in use relied on [fake]root.) * Fix usage of default Debian build flags: Use buildflags.mk with appropriate _APPEND settings, and tweak hardening.patch to add DEB_*FLAGS to the front rather than the end (so as to keep upstream's preferred optimization level). * Preclean more fully to allow for consecutive builds. * List (wildcard) currently uninstalled files in debian/not-installed. * Correct logic for identifying all failing tests when there are any. * Secure URI in copyright format (routine-update) * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine- update) * Remove trailing whitespace in debian/changelog (routine-update) * Remove trailing whitespace in debian/rules (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Add myself to uploaders. -- Aaron M. Ucko Wed, 20 May 2020 22:15:19 -0400 sra-sdk (2.9.4+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version. * Bumped policy to 4.3.0 -- Steffen Moeller Tue, 26 Feb 2019 15:01:51 +0100 sra-sdk (2.9.3+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version. -- Steffen Moeller Tue, 23 Oct 2018 15:12:22 +0200 sra-sdk (2.9.2+dfsg-2) unstable; urgency=medium * Architecture: amd64 -- Andreas Tille Fri, 14 Sep 2018 08:24:15 +0200 sra-sdk (2.9.2+dfsg-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.2.1 -- Andreas Tille Mon, 10 Sep 2018 08:25:37 +0200 sra-sdk (2.9.1-1+dfsg-2) unstable; urgency=medium * Team upload. * Set Build-Depends: libncbi-vdb-dev (>=2.9.1) to avoid undefined symbol errors -- Liubov Chuprikova Thu, 05 Jul 2018 19:13:15 +0300 sra-sdk (2.9.1-1+dfsg-1) unstable; urgency=medium * Team upload [ Andreas Tille ] * New upstream version * debhelper 11 * New Build-Depends: libvdb-sqlite-dev, versioned Build-Depends libncbi-vdb-dev (>= 2.9.0) * Exclude strangely failing test align-cache (needs investigation) [ Liubov Chuprikova ] * Add autopkgtest * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 -- Liubov Chuprikova Sun, 01 Jul 2018 08:22:54 +0200 sra-sdk (2.8.2-5+dfsg-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.1.3 -- Andreas Tille Sun, 18 Feb 2018 15:44:10 +0100 sra-sdk (2.8.2-3+dfsg-1) unstable; urgency=medium [ Steffen Moeller ] * debian/upstream/metadata: - added references to registries - yamllint cleanliness [ Andreas Tille ] * New upstream version * cme fix dpkg-control * Standards-Version: 4.1.1 * debhelper 10 * renamed function to resolve name clash with gnutards to avoid FTBFS with glibc 2.25 Closes: #882349 * Drop test that should not run as root -- Andreas Tille Mon, 04 Dec 2017 08:29:02 +0100 sra-sdk (2.8.1-2+dfsg-2) unstable; urgency=medium * Fix install dir by using DEB_HOST_MULTIARCH instead of DEB_BUILD_GNU_TYPE (thanks for the patch to Graham Inggs ) Closes: #859261 -- Andreas Tille Sat, 01 Apr 2017 23:06:00 +0200 sra-sdk (2.8.1-2+dfsg-1) unstable; urgency=medium * New upstream bugfix release -- Andreas Tille Tue, 24 Jan 2017 09:05:43 +0100 sra-sdk (2.8.1+dfsg-3) unstable; urgency=medium * Upstream suggested a different name to resolve #851219: vdb-get -- Andreas Tille Sat, 14 Jan 2017 14:41:57 +0100 sra-sdk (2.8.1+dfsg-2) unstable; urgency=medium * Deal with name space conflict with kget Closes: #851219 -- Andreas Tille Fri, 13 Jan 2017 09:23:03 +0100 sra-sdk (2.8.1+dfsg-1) unstable; urgency=medium * New upstream version Closes: #846461 * For whatever reason configure is checking for libfuse-dev so add it to Build-Depends * Build-Depends: libhdf5-dev, libmagic-dev, libxml2-dev -- Andreas Tille Wed, 11 Jan 2017 23:06:42 +0100 sra-sdk (2.7.0-2) unstable; urgency=medium * d/rules: Remove -pie to adapt to latest changes in dpkg * link against Debian packaged libmbedtls-dev * Enable build using ncbi-vdb version 2.8.0 -- Andreas Tille Fri, 25 Nov 2016 19:08:25 +0100 sra-sdk (2.7.0-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version Closes: #680436, #769050 * d/watch points to github * d/copyright: no need to exclude any files any more * cme fix dpkg-control * New Build-Depends: libhdf5-dev, libngs-sdk-dev (>= 1.2.4) * drop library packages since these are now build by ncbi-vdb * use Github as homepage [ Steffen Moeller and Jon Ison ] * Introduced EDAM annotation to debian/upstream/edam -- Andreas Tille Thu, 01 Sep 2016 15:41:02 +0200 sra-sdk (2.3.5-2+dfsg-1) unstable; urgency=medium * New upstream version * d/rules: Adapt get-orig-source target to new uscan implementation * d/watch: use uversionmangle to get properly named download tarball -- Andreas Tille Wed, 30 Jul 2014 13:52:45 +0200 sra-sdk (2.3.4-2+dfsg-2) unstable; urgency=medium * delete symbols file Closes: #736411 * lintian override for no-symbols-control-file -- Andreas Tille Thu, 23 Jan 2014 13:41:59 +0100 sra-sdk (2.3.4-2+dfsg-1) unstable; urgency=medium * New upstream version * debian/control: - Add missing Depends: sra-toolkit-libs0 to sra-toolkit-libs-dev Closes: #715133 - Standards-Version: 3.9.5 (no changes needed) * debian/sra-toolkit-libs0.symbols: Adapted to new upstream version -- Andreas Tille Mon, 23 Dec 2013 22:27:00 +0100 sra-sdk (2.3.3-4~dfsg-1) unstable; urgency=low [ Andreas Tille ] * New upstream version * debian/upstream: Add citation information * fix debian/watch * debian/control: - cme fix dpkg-control - debhelper 9 - canonical Vcs fields * debian/copyright: Exclude external libraries * debian/rules: - Add get-orig-source target to call enhances uscan - remove override because upstream seems to do the correct thing now - libsra-schema seems to be not built any more in this version so drop the special handling of it - Reactivate deletion of libs/krypto/*.pic.o.list files to get a really clean source * debian/doc: USAGE is not provided by upstream any more * debian/patches/build-with-system-libbz2-libz.patch: Fix build problem (thanks to Gert Wollny for the patch) * debian/sra-toolkit.install: There are neither mod?? nor wmod?? files shipped in this version any more - so remove these from dh_install * debian/patches/hardening.patch: Propagate Debian hardening options into build system * debian/patches/hardening-format-security.patch: Fix format strings in snprintf() calls * debian/watch: mangle version string * debian/sra-toolkit-libs0.lintian-overrides: override package-name-doesnt-match-sonames [ Charles Plessy ] 32dd5cd Updated symbols file. -- Andreas Tille Wed, 23 Oct 2013 10:43:20 +0200 sra-sdk (2.1.7a-1) unstable; urgency=low [ Charles Plessy ] 61e22aa New upstream release (Closes: #627861). 1b09fd5 Normalised debian/copyright file with config-edit. a93e7b5 Wildcard characters to match 64 or 32 according to the architecture. 3d66d80 New upstream source location in debian/watch. 74e5234 Mark the use of git-buildpackage by debian/gbp.conf. 0074d68 Simplified Homepage URL in debian/control. 5cd8039 Use a target that allows dynamic linking (debian/rules). 9815817 Do not install empty /usr/bin/ncbi directory (debian/rules). fb42792 Updated debian/sra-toolkit-libs0.symbols. 866f773 Install config.kfg and vdb-copy.kfg in /etc/ncbi. [ Andreas Tille ] 9e6e831 Suggest patches for build system to build on non i386&amd64 architectures as well as BSD and Hurd -- Charles Plessy Tue, 10 Jan 2012 09:06:14 +0900 sra-sdk (2.0.1-1) unstable; urgency=low * Initial release (Closes: #610603). -- Charles Plessy Tue, 24 May 2011 14:48:10 +0900