ncbi-vdb (3.0.9+dfsg-2) unstable; urgency=medium * Upload to unstable to join Mbed TLS 3.x. (Closes: #1075868.) * debian/salsa-ci.yml: Comment out aptly setup, no longer needed. -- Aaron M. Ucko Thu, 17 Oct 2024 22:35:54 -0400 ncbi-vdb (3.0.9+dfsg-1) experimental; urgency=medium [ Andreas Tille ] * New upstream version [ Aaron M. Ucko ] * debian/control: Version libmbedtls-dev B-D to (>= 3), so far available only in experimental, to match recent versions' usage. * debian/patches/system_mbedtls_3.patch (new): Reinstate test for system mbed TLS, tweaking it to accept (and moreover require) 3.x. * debian/salsa-ci.yml: Reenable aptly per the need to target experimental again for now. -- Aaron M. Ucko Thu, 11 Apr 2024 17:40:20 -0400 ncbi-vdb (3.0.2+dfsg-2) unstable; urgency=medium * Upload to unstable. * debian/salsa-ci.yml: Stop reenabling aptly, no longer needed. -- Aaron M. Ucko Fri, 20 Jan 2023 17:43:12 -0500 ncbi-vdb (3.0.2+dfsg-1) experimental; urgency=medium * New upstream release. * debian/control: Drop libkdf5-* and corresponding libhdf5-dev build-dep. * debian/copyright: Drop references to content removed upstream, both in Files-Excluded and in special cases. * debian/patches: Refresh for 3.0.{1,2}(+dfsg); many of our changes can go away now that upstream supports using system mbed TLS. (The only difference between 3.0.1 and 3.0.2 is a formal version bump to sync with sra-tools 3.0.2.) * debian/rules: Account for upstream library installation changes: - Honoring CMAKE_INSTALL_LIBDIR (which specifies multiarch paths). - Dropping several static libraries (which had been installed on principle). - Dropping libkdf5. * Standards-Version: 4.6.2 (routine-update) -- Aaron M. Ucko Tue, 27 Dec 2022 12:01:29 -0500 ncbi-vdb (3.0.0+dfsg2-4) experimental; urgency=medium * debian/control: - Drop i386, desupported upstream. - Formally clean up per cme fix. * debian/rules: Use $(DEB_HOST_ARCH_BITS) in LIBINSTALLDIR for the sake of x32. * debian/salsa-ci.yml: Enable aptly for the sake of sra-sdk 3.x until both packages return to unstable. -- Aaron M. Ucko Mon, 14 Nov 2022 21:30:44 -0500 ncbi-vdb (3.0.0+dfsg2-3) experimental; urgency=medium * .gitignore: Ignore temporary interfaces/cc/gcc/aarch64 symlink. * debian/patches/detect_BITS.patch (new): Base BITS on sizeof(void *). This change is particularly helpful on x32, which the build system otherwise conflates with x86_64. * debian/patches/fix_cmake.patch: Explicitly link mbedtls's dependencies. They see some direct usage. * debian/patches/fix_x32.patch (new): Fully fix x32 builds. In particular, don't try to build test-wvdb-slow when the address space is only 32 bits wide. * debian/rules: - Unhardcode architecture component in chrpath call. - Address arm64/aarch64 header path mismatch with a symlink. -- Aaron M. Ucko Thu, 01 Sep 2022 23:01:22 -0400 ncbi-vdb (3.0.0+dfsg2-2) experimental; urgency=medium * debian/.gitignore: Also ignore common-install-stamp. * debian/control: Split out Build-Depends-Arch, for nearly everything. * debian/patches/fix_cmake.patch: Link libncbi-(w)vdb.so against all dependencies. (Leave the test subtree's COMMON_LIBS_* settings alone because tests link statically.) * debian/rules: Accommodate builds covering only architecture-dependent or architecture-independent packages, with the help of a new debian/common-install-stamp target. -- Aaron M. Ucko Fri, 26 Aug 2022 08:08:33 -0400 ncbi-vdb (3.0.0+dfsg2-1) experimental; urgency=medium * Merge (or port, as appropriate) changes from 2.11.2+dfsg-5. - Account for changes to the binary package inventory. - Account for layout changes. - Extend upstream's copyright through 2022. * .gitignore: Also ignore obj-* and test/vdb/kfg/*/user-settings.mkfg. * debian/control: Drop unneeded build dependencies: libngs-* and default-jdk-headless. Keeping libngs-* would have resulted in a dependency cycle with sra-sdk 3.x (which incorporates ngs-sdk), and default-jdk-headless is heavy. * debian/copyright: Additionally exclude */vdb3/jwt-tool/googletest, which came to my attention over formal line-ending mismatches relative to the tarball (specifically in Visual Studio files). * debian/rules: Clean up fully between builds. * debian/watch: Adjust dversionmangle to allow digits after +dfsg, per the use of +dfsg2 for now. -- Aaron M. Ucko Thu, 25 Aug 2022 00:55:47 -0400 ncbi-vdb (3.0.0+dfsg-1) experimental; urgency=medium * New upstream version * Switch to cmake build system * Reflect SONAME bump in package names * Library libvdb-sqlite is not provided by upstream any more which builds libsam-extract as new library. Binary packages are adapted accordingly * Review copyright * Remove RPATH * Standards-Version: 4.6.1 -- Andreas Tille Sat, 19 Feb 2022 11:53:03 +0100 ncbi-vdb (2.11.2+dfsg-5) unstable; urgency=medium * .gitignore: Also ignore libs/jni/jni(_md).h. * debian/.gitignore (new): Ignore generated files and subtrees. * debian/control: - Clean up descriptions. In particular, use a modern synopsis cribbed from vdb3/README.md as a first paragraph across the board. - Note that all packages already qualify as Multi-Arch: same. - Introduce ncbi-vdb-data (M-A: foreign) and have libncbi-(w)vdb2 depend on it. * debian/copyright: - Resync details with tarball contents. - Stop claiming Upstream-Name: ngs. * debian/ncbi-vdb-data.install: Rename from libncbi-vdb2.install. (It listed only default configuration files, with d-shlibs taking care of the rest.) * debian/rules: Move schemata to ncbi-vdb-data, not libncbi-vdb2. * Standards-Version: 4.6.1 (routine-update) -- Aaron M. Ucko Wed, 24 Aug 2022 14:26:20 -0400 ncbi-vdb (2.11.2+dfsg-4) unstable; urgency=medium * zstd.patch: Adopt dynamic system zstd more fully. - Comment out ZSTD_STATIC_LINKING_ONLY to enforce use of stable APIs. - Actually link libncbi-(w)vdb and libvdb-sqlite against libzstd. * Have libncbi-vdb2 break sra-toolkit (<< 2.11) anyway -- even with zstd linkage fixed, sra-toolkit 2.10.x's autopkgtest will still fail over dropped support for protected repository configuration. -- Aaron M. Ucko Mon, 22 Nov 2021 22:39:27 -0500 ncbi-vdb (2.11.2+dfsg-3) unstable; urgency=medium * Leave mbedtls quirk handling to d-shlibs (>= 0.104). (Closes: #999788.) * Skip VDB3, at least for now -- it FTBFS on i386, and has so far just been an uninstalled technology preview. * Enable arm64 builds. To that end: - add_-msse2.patch: Limit -msse2 to 32-bit x86. (Redundant on 64-bit x86, invalid elsewhere.) - debian/rules: Wildcard upstream architecture name (VDB_ARCH), no longer consistently aligned with any single dpkg-architecture variable. * debian/watch: Track tags rather than releases, of which GitHub no longer lists any(!). -- Aaron M. Ucko Sat, 20 Nov 2021 23:06:09 -0500 ncbi-vdb (2.11.2+dfsg-2) unstable; urgency=medium * Binary package libncbi-vdb-dev Depends: libzstd-dev -- Andreas Tille Mon, 01 Nov 2021 16:56:26 +0100 ncbi-vdb (2.11.2+dfsg-1) unstable; urgency=medium * Fix watchfile to detect new versions on github * New upstream version * Standards-Version: 4.6.0 (routine-update) * Remove trailing whitespace in debian/changelog (routine-update) * Build-Depends: cmake * Use Debian packaged libzstd * Fix missing cstdlib include * Add more files to debian/not-installed * Drop RFCs from package source -- Andreas Tille Mon, 11 Oct 2021 14:16:45 +0200 ncbi-vdb (2.10.9+dfsg-2) unstable; urgency=medium * d/p/fix_2.10.9_refseq_race.patch: Fix a new race in asynchronous RefSeq loading code, per upstream (https://github.com/ncbi/ncbi-vdb) commits 06152a5, cf92dca, and b342af2. -- Aaron M. Ucko Mon, 18 Jan 2021 16:57:54 -0500 ncbi-vdb (2.10.9+dfsg-1) unstable; urgency=medium * New upstream version * d/watch: Use filemangle to make sure the archive will not mixed up with other ncbi code with same version * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) -- Andreas Tille Mon, 18 Jan 2021 08:27:11 +0100 ncbi-vdb (2.10.7+dfsg-1) unstable; urgency=medium * New upstream version * Remove trailing whitespace in debian/changelog (routine-update) * debian/not-installed: Update for new release (more test-related files). -- Aaron M. Ucko Tue, 02 Jun 2020 21:35:11 -0400 ncbi-vdb (2.10.6+dfsg-5) unstable; urgency=medium * Comment out fix_parallel_build.patch (evidently insufficient) in favor of overriding dh_prep to spare(!) debian/tmp. * optionally_reinstate_default_schema.patch: Use plain extern rather than SRA_EXTERN to avoid likely multiple definitions under GCC 10. -- Aaron M. Ucko Tue, 26 May 2020 10:32:22 -0400 ncbi-vdb (2.10.6+dfsg-4) unstable; urgency=medium * debian/patches/fix_parallel_build.patch (new): Use unique temporary directory names when combining static libraries. -- Aaron M. Ucko Tue, 26 May 2020 08:06:35 -0400 ncbi-vdb (2.10.6+dfsg-3) unstable; urgency=medium * debian/patches/optionally_reinstate_default_schema.patch: New patch to let callers use the default schema, otherwise dropped upstream as of 2.10.0. (The toggle is a new global variable SRAUseLegacyDefaultSchema, which sra-sdk's tools/sra-load will enable to address the autopkgtest failure #961347.) -- Aaron M. Ucko Mon, 25 May 2020 22:38:23 -0400 ncbi-vdb (2.10.6+dfsg-2) unstable; urgency=medium * Install libs/vfs/services-priv.h as .../services-priv-internal.h to distinguish it from interfaces/vfs/services-priv.h. (Neither can stand in for the other.) * Formally refresh patches that developed offsets. * Factor out a new DSLMFLAGS macro for common d-shlibmove flags; include the libmbedx509-0 quirk there since it will soon be needed everywhere. * Address remaining underlinkage of system libraries (mbed*, z, bz2). At this point, the only remaining unresolved references are of libkdf5 against symbols that could come from either libncbi-vdb or libncbi-wvdb. (Closes: #952623, #952627, #953897.) * Copy headers rather than moving them to allow for consecutive builds. * Fix typo in override_dh_missing name; supply debian/not-installed. * Add myself to Uploaders. -- Aaron M. Ucko Wed, 20 May 2020 22:13:24 -0400 ncbi-vdb (2.10.6+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version * Rules-Requires-Root: no (routine-update) -- Steffen Moeller Mon, 18 May 2020 23:55:32 +0200 ncbi-vdb (2.10.5+dfsg-1) UNRELEASED; urgency=medium * New upstream version [ Andreas TIlle ] * Try even harder to get rid of vdb_mbedtls symbols [ Michael R. Crusoe ] * Update mbedtls patches to 2.10.5 and consolidate them -- Steffen Moeller Mon, 02 Mar 2020 02:04:31 +0100 ncbi-vdb (2.10.3+dfsg-2) unstable; urgency=medium * Removed additional invocations of vdb_mbedtls to avoid undefined references when linking against vdb. -- Steffen Moeller Mon, 02 Mar 2020 01:12:48 +0100 ncbi-vdb (2.10.3+dfsg-1) unstable; urgency=medium [ Steffen Moeller ] * New upstream version * debhelper-compat 12 (routine-update) * Adjusted patches. [ Andreas Tille ] * Standards-Version: 4.5.0 * Architecture: amd64 i386 x32 Closes: #950737 * New upstream version * Add salsa-ci file (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. -- Andreas Tille Mon, 24 Feb 2020 21:49:23 +0100 ncbi-vdb (2.9.3+dfsg-2) unstable; urgency=medium * Replace remainin occurrence of vdb_mbedtls_ssl_conf_authmode by mbedtls_ssl_conf_authmode Closes: #919306 -- Andreas Tille Mon, 14 Jan 2019 21:54:31 +0100 ncbi-vdb (2.9.3+dfsg-1) unstable; urgency=medium * New upstream version * debhelper 12 * Standards-Version: 4.3.0 -- Andreas Tille Fri, 11 Jan 2019 23:15:24 +0100 ncbi-vdb (2.9.2-1+dfsg-1) unstable; urgency=medium * New upstream version [ Steve Langasek ] * add missing implementation of uint64_msbit for i386 Closes: #907358 [ Andreas Tille ] * d/rules: - DEB_LDFLAGS_MAINT_APPEND := -Wl,--as-needed - Considered using DEB_LDFLAGS_MAINT_APPEND := -Wl,-z,defs which should prevent successful build of a broken library (thanks for the hint to Steve Langasek) Unfortunately this uncovers several other build failures - volunteers to provide the correct linker flags are welcome - dh_auto_build --no-parallel * Standards-Version: 4.2.1 -- Andreas Tille Tue, 04 Sep 2018 14:14:44 +0200 ncbi-vdb (2.9.1-1+dfsg-1) unstable; urgency=medium * New upstream version * Fixes accidental ABI break in 2.9.1 Closes: #902566 -- Andreas Tille Thu, 28 Jun 2018 05:41:16 +0200 ncbi-vdb (2.9.1+dfsg-1) unstable; urgency=medium * New upstream version * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 -- Andreas Tille Wed, 27 Jun 2018 21:41:56 +0200 ncbi-vdb (2.9.0-1+dfsg-2) unstable; urgency=medium * Drop some unneeded d-shlibs overrides available in version 0.82 * New library package libvdb-sqlite2 / libvdb-sqlite-dev featuring the sqlite interface -- Andreas Tille Sun, 01 Apr 2018 14:53:23 +0200 ncbi-vdb (2.9.0-1+dfsg-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.1.3 * debhelper 11 * d/rules: s/DEB_BUILD_OPTIONS/DH_BUILD_MAINT_OPTIONS/ -- Andreas Tille Mon, 19 Mar 2018 11:36:13 +0100 ncbi-vdb (2.8.2-2+dfsg-1) unstable; urgency=medium * New upstream version * cme fix dpkg-control * Standards-Version: 4.1.1 * More adaptations to Debian packaged libmbedx * d/rules: Do not parse changelog * Try better hardening -- Andreas Tille Thu, 19 Oct 2017 23:40:15 +0200 ncbi-vdb (2.8.1+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: #859260 -- Andreas Tille Sat, 01 Apr 2017 22:50:01 +0200 ncbi-vdb (2.8.1+dfsg-1) unstable; urgency=medium * New upstream version * Install libs/kfg/*.kfg into /usr/lib/ncbi-vdb/kfg/ -- Andreas Tille Wed, 11 Jan 2017 15:27:16 +0100 ncbi-vdb (2.8.0+dfsg-2) unstable; urgency=medium * Make sure libraries are properly linked with libmbed Closes: #844900 * Adjust dependencies from other development packages * debhelper 10 * d/watch: version=4 -- Andreas Tille Fri, 25 Nov 2016 12:41:49 +0100 ncbi-vdb (2.8.0+dfsg-1) unstable; urgency=medium * New upstream version * Use wildcard instead of $(CPU) in install to fix FTBFS on i386 (thanks for the patch to Logan Rosen ) Closes: #843129 * New Build-Depends: libmbedtls-dev -- Andreas Tille Fri, 04 Nov 2016 10:15:13 +0100 ncbi-vdb (2.7.0+dfsg-4) unstable; urgency=medium * Fix schema paths -- Andreas Tille Thu, 01 Sep 2016 11:49:14 +0200 ncbi-vdb (2.7.0+dfsg-3) unstable; urgency=medium * Fix build on i386 (Thanks to Aaron M. Ucko for the hint) -- Andreas Tille Thu, 01 Sep 2016 09:37:50 +0200 ncbi-vdb (2.7.0+dfsg-2) unstable; urgency=medium * Enable build on x32 by removing explicit -m32/-m64 Closes: #836129 * Add -msse2 to libs/search Closes: #836128 -- Andreas Tille Wed, 31 Aug 2016 08:36:36 +0200 ncbi-vdb (2.7.0+dfsg-1) unstable; urgency=medium * Initial release (Closes: #832165) -- Andreas Tille Mon, 25 Jul 2016 12:20:14 +0200