sra-sdk (3.0.3+dfsg-6~deb12u1) bookworm; urgency=medium * Reupload to bookworm (stable). -- Aaron M. Ucko Thu, 13 Jul 2023 23:08:59 -0400 sra-sdk (3.0.3+dfsg-6) unstable; urgency=high * debian/rules: Expand $(DEB_HOST_MULTIARCH) in libngs-java.links.in. (Closes: #1039621.) -- Aaron M. Ucko Tue, 27 Jun 2023 22:14:41 -0400 sra-sdk (3.0.3+dfsg-5) unstable; urgency=medium * Limit libngs-java to those architectures where libs are available Closes: #1031853 * DEP3 for all patches -- Andreas Tille Fri, 24 Feb 2023 11:52:27 +0100 sra-sdk (3.0.3+dfsg-4) unstable; urgency=medium * debian/rules: Explicitly build with signed characters (-fsigned-char). On arm64, where char is normally unsigned, two tests otherwise fail because messages reporting certain characters' numeric values formally differ from expectations. -- Aaron M. Ucko Sun, 22 Jan 2023 17:04:21 -0500 sra-sdk (3.0.3+dfsg-3) unstable; urgency=medium * debian/copyright: Account for a second(!) version of BitMagic under tools/loaders/bam-loader, with copyright running through 2022. * debian/patches/no_sse4.2.patch (new): Don't use SSE 4.2. It's a baseline violation on x86, and entirely unavailable elsewhere. * debian/patches/use_c_locale_for_comma (new): Stick with the C locale. en_US.UTF-8 isn't necessarily available, particularly on the buildds, and C is perfectly sufficient to ensure recognition of comma as a thousands separator. (Recent versions of glibc supply a middle-ground C.utf8, but even that looks like overkill at the moment.) -- Aaron M. Ucko Sun, 22 Jan 2023 13:26:16 -0500 sra-sdk (3.0.3+dfsg-2) unstable; urgency=medium * Upload to unstable. * .gitignore: Update patterns corresponding to test output. * debian/control: - Drop vestigial versioned dependency on libncbi-wvdb2. - Limit architecture-dependent packages to amd64 and arm64. The only other architecture ncbi-vdb supports is x32, but these tools require a 64-bit address space. * debian/not-installed: Refresh. - Correct location of explicitly tagged lib*-static.a. - Drop spurious entries (with hardcoded amd64 paths, no less). * debian/patches/fix_ngs-c++-underlinkage.patch (new): Link libngs-c++ against all internal dependencies. Hold off for now on linking against libncbi-vdb, though anyone looking to substitute libncbi-wvdb would need to contrive to supply a suitable definition of KDBManagerMakeRead. * debian/patches/label_online_tests.patch: Extend as needed. All existing labels confirmed to remain appropriate. * debian/patches/link_vdb_dynamically.patch: Extend prior to building tests again. To wit, additionally cover makeinputs, from tools/loaders/general-loader/test. (All other tests were already OK at this point.) * debian/patches/prefer_dynamic_libraries.patch: Comment out upstream logic that favored static linkage. * debian/rules: - Skip rpaths, not needed even for libhdf5. - Explicitly enable tests, disabled by default these days. - Update test cleanup logic to allow for build area reuse. * debian/salsa-ci.yml: Retire remaining customizations. -- Aaron M. Ucko Fri, 20 Jan 2023 17:57:36 -0500 sra-sdk (3.0.3+dfsg-1) experimental; urgency=medium [ Andreas Tille ] * Breaks+Replaces: libncbi-vdb-dev (<< 3), libngs-sdk-dev (<< 3) Closes: #1024155 [ Aaron M. Ucko ] * New upstream version. * .gitignore: - Unhardcode architecture name in build tree (obj-*). - Ignore build results under ngs/ngs-python (dist, ngs.egg-info). * debian/{control,salsa-ci.yml}: Build against libncbi-vdb-dev 3.0.1+. * debian/copyright: Account for layout changes as of 3.0.1 and drop references to content removed upstream, both in Files-Excluded and in special cases. * debian/patches: Update for 3.0.1+; in particular, account for layout changes and better support for using system libraries. * debian/rules: - Correctly accommodate multiple supported Python versions. (I'd insufficiently adapted ncbi-ngs's relevant logic.) - Account for layout changes and CMAKE_INSTALL_LIBDIR support (with the latter yielding multiarch paths). - Clean up newly generated files under ngs/ngs-python. * debian/{rules,sra-toolkit.install}: Move sratools and *-orig to a new /usr/lib/sra-toolkit directory; repoint symlinks accordingly. (Closes: #1025278.) * Standards-Version: 4.6.2 (routine-update) -- Aaron M. Ucko Wed, 18 Jan 2023 21:42:39 -0500 sra-sdk (3.0.0+dfsg-1) experimental; urgency=medium [ Andreas Tille ] * New upstream version * Standards-Version: 4.6.1 (routine-update) * Build-Depends: default-jdk, flex, bison [ Aaron M. Ucko ] * debian/control: - Account for consolidation of ngs-sdk (albeit with some intervening changes, notably library restructuring); take the opportunity to add a -java-doc package.0 - Let python3-ngs bypass libncbi-ngs-dev and use libncbi-ngs3 directly. - Drop build dependency on libvdb-sqlite-dev, now internal to sra-sdk. * debian/libngs-java-doc.javadoc: Enable javadoc installation. * debian/{libngs-java.{jlibs,poms},ngs-java.pom(.asc)}: Adopt (and adapt) from ngs-sdk. * debian/*ngs*.examples (new): Install upstream NGS examples. * debian/not-installed: Ignore usr/jar/*.jar (installed elsewhere, via jh_installlibs), usr/lib64/lib*-static.a, usr/share/examples* (installed elsewhere, via dh_installexamples), and usr/share/javadoc/ngs-doc (installed elsewhere, via jh_installjavadoc). * debian/patches/use_debian_packaged_re2.patch: Comment out an inappropriate add_dependencies call in test/sharq/CMakeLists.txt. * Add more patches for remaining build issues: fix_javadoc_build.patch, link_magic_dynamically.patch, link_vdb_dynamically.patch, and use_debian_packaged_compression_libs.patch. * debian/patches/use_soversions.patch (new): Give shared libraries proper versioned SONAMEs; use them from the Python bindings. * debian/rules: - Adopt (and adapt) assorted build logic from ngs-sdk. - Pass VDB header path via -DVDB_INCDIR rather than via general compilation flags. - Install configuration files explicitly; the CMake setup insists on putting them in the wrong place for us. - Extend bin deversioning to *+ (i.e., kar+). * debian/salsa-ci.yml: Use ncbi-vdb's aptly repo to get 3.x for now. [ Pierre Gruet ] * debian/control: - Add missing build dependencies on liblzma-dev and libsam-extract-dev. - Mark libngs-java as Architecture: all; loosen its dependencies on libncbi-ngs-dev slightly to account for possible binNMUs. - Introduce a libngs-jni package, on which libngs-java can and will depend in lieu of libncbi-ngs-dev (or patching source to support using libncbi-ngs3 directly). * debian/libngs-java-doc.lintian-overrides: Override complaints about javadoc-embedded jQuery per the discussion starting at https://lists.debian.org/debian-java/2018/06/msg00020.html. * debian/libngs-jni.links.in: Provide a general formula for libngs-jni's central symlink. * debian/rules: Add logic to fill in the specifics. [ Aaron M. Ucko ] * (debian/).gitignore (new): Ignore build and (offline) test results. * debian/control: - Make python3-ngs (safely!) Architecture: all too. - Attempt Architecture: any for sra-toolkit (modulo B-D availability). This setting matches architecture-dependent NGS packages'; if it doesn't work out, we'll want to rein them all in for simplicity. - Honor ${misc:Depends} for libngs-java per Lintian. * debian/copyright: Reflect a full inventory, including convenience copies of several third-party libraries for which it would be good to substitute existing packages at some point. * debian/patches/label_online_tests (new): Label tests that involve data retrieval as "online". * debian/patches/reflect_code_donations.patch (new): Clean up stray licenseless copyright statements per consultation with upstream (as quoted in the patch's header). * debian/patches/use_stock_magic.patch (new): Let copycat use the stock magic-number database in /usr/share/misc. * debian/rules: - Skip tests labeled "online" to avoid breaking on autobuilders, which require builds to work fully offline. - Refrain from shipping .gitignore files alongside examples. - Clean up after tests (offline ones, anyway). * Remove trailing whitespace in debian/changelog (routine-update) -- Aaron M. Ucko Sun, 13 Nov 2022 22:22:28 -0500 sra-sdk (2.11.3+dfsg-1) unstable; urgency=medium [ Andreas Tille ] * Fix watchfile to detect new versions on github * New upstream version 2.11.2. * Standards-Version: 4.6.0 (routine-update) * Bump versioned Build-Depends: libngs-sdk-dev (>= 2.11.2) * Skip test that test needs a *lot* of memory * Link against libzstd. (Closes: #997280.) [ Aaron M. Ucko ] * d/p/fix_libngs_linkage.patch (new): Substitute ngs-c++ library for absent ngs library. * debian/rules: Stop renaming kget (to avoid a file conflict, #851219) now that it's retired altogether. * d/p/allow_multi_help.patch (new): Tolerate redundant --help declarations within tools/driver-tool. * d/p/run_unversioned_tools.patch (new): Look for tools by their unversioned names, per Debian's simplified installation arrangement. * debian/tests: Switch to modern encryption/decryption setup. - run-unit-test: Replace protected repository configuration (no longer supported as of ncbi-vdb 2.11.0) by --ngc [...].ngc. - test-data.tar.gz: Replace dbGaP-0.enc_key by a copy of upstream's test/prefetch/data/prj_phs710EA_test.ngc. * debian/watch: Look for tags rather than releases, as GitHub currently lists none(!) of the latter. * New upstream version 2.11.3. -- Aaron M. Ucko Mon, 25 Oct 2021 18:29:10 -0400 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