ncbi-blast+ (2.16.0+ds-7) unstable; urgency=medium

  * debian/control: Build-depend on libncbi-vdb-dev where available
    (amd64, arm64, and x32).
  * debian/copyright: Overhaul with much help from licenserecon (lrc).
  * debian/patches/fix_bm_for_gcc15 (new): Cherry-pick a BitMagic fix
    needed for modern compilers, adjusting the path appropriately.'
    (Closes: #1097434.)
  * debian/rules: Build against (packaged!) VDB where available, using
    logic cribbed from ncbi-igblast.  (Closes: #1100037.)
  * Standards-Version: 4.7.2 (routine-update)

 -- Aaron M. Ucko <ucko@debian.org>  Sat, 03 May 2025 23:42:51 -0400

ncbi-blast+ (2.16.0+ds-6) unstable; urgency=medium

  * debian/control: Reinstate big-endian builds, which can be salvaged
    adequately well.
  * debian/patches/big_endian_workaround (new): On big-endian
    architectures, roll makeblastdb's and makeprofiledb's default
    blastdb_version back to 4 pending a proper fix.  Some things,
    including in particular q2-feature-classifier, will still explicitly
    request version 5, but everything else should be OK.  (See #1077777.)
  * debian/rules: Try disabling optimization altogether on sh4.

 -- Aaron M. Ucko <ucko@debian.org>  Tue, 06 Aug 2024 21:45:09 -0400

ncbi-blast+ (2.16.0+ds-5) unstable; urgency=medium

  * debian/control: Forbid builds for big-endian architectures, at least
    for now.  They nominally succeed, but two dependent autopkgtests (for
    cct and kleborate) have started failing on s390x, and there's no
    evidence that other BE architectures fare any better.  (See #1077777.)
  * debian/rules:
    - Try building with -fsection-anchors on alpha in hopes of satisfying
      the GOT size limit there too.
    - Extend -O1 cap to sh4, which still encountered VM exhaustion.

 -- Aaron M. Ucko <ucko@debian.org>  Sun, 04 Aug 2024 16:04:32 -0400

ncbi-blast+ (2.16.0+ds-4) unstable; urgency=medium

  * debian/rules:
    - Move architecture.mk inclusion to the very top for the sake of
      hypothetical builds bypassing dpkg-buildpackage.
    - Compile with -ffunction-sections on hppa and -mxgot on mips*
      (mips64el in practice) due to having outgrown default settings.
    - Disable parallel building on sh4 in hopes of avoiding buildd virtual
      memory exhaustion.

 -- Aaron M. Ucko <ucko@debian.org>  Sat, 27 Jul 2024 22:38:52 -0400

ncbi-blast+ (2.16.0+ds-3) unstable; urgency=medium

  * debian/rules: Fix typo (missing parenthesis).

 -- Aaron M. Ucko <ucko@debian.org>  Fri, 26 Jul 2024 15:37:28 -0400

ncbi-blast+ (2.16.0+ds-2) unstable; urgency=medium

  * debian/patches/hurd_fixes: Extend to ncbi_localip.c, which otherwise
    accommodates PATH_MAX's absence only under Windows.
  * debian/rules: Link with -latomic on most 32-bit architectures
    (excepting only x86 and armhf, which succeed as is).

 -- Aaron M. Ucko <ucko@debian.org>  Fri, 26 Jul 2024 14:54:55 -0400

ncbi-blast+ (2.16.0+ds-1) unstable; urgency=medium

  * New upstream release, which should be (more than) new enough for
    recent q2-feature-classifier.  (Closes: #1074316.)
  * debian/control:
    - Build against libnghttp2-dev, libsqlite3-dev, and libuv1-dev, newly
      needed.
    - Build against autoconf2.69.
    - Build against libpcre2-dev, as enabled by debian/patches/allow_pcre2.
    - Stop building against 2to3, which may not be around much longer.
  * debian/patches: Update for new release, mostly formally.
  * debian/patches/2to3 (new): Cache 2to3 diff for
    windowmasker_2.2.22_adapter.
  * debian/patches/allow_pcre2 (new): Allow use of PCRE2.
  * debian/patches/series:
    - Move system_mbedtls_only up in conjunction with incorporating part
      of an upstream patch needed by support_mbedtls3.
    - Comment out reprobuild; I'm all for reproducibility, but the package
      already automatically builds with flags that make __FILE__ relative,
      and many of its uses are in header-defined macros that intend to
      pick up their callers' paths.
  * debian/patches/support_mbedtls3 (new): Support (but don't require)
    Mbed TLS 3.x.  (Closes: #1075867.)
  * debian/patches/system_mbedtls: Extend to cover ncbi_mbedtls.c (as in
    https://github.com/ncbi/ncbi-cxx-toolkit-public/commit/f9c7297dd1)
    and Makefile.xxconnect2.lib.
  * debian/rules:
    - Regenerate configure and config.h.in with Autoconf 2.69.
    - Build against PCRE2, as enabled by debian/patches/allow_pcre2.
      (Closes: #891197.)
    - Tune flags: Add --without-strip to make --with-symbols effective;
      switch off warnings from __DATE__/__TIME__ usage, since
      dpkg-buildpackage's SOURCE_DATE_EPOCH injection should suffice.
    - Extend generated-sources cleanup to objtools/eutils (not entirely
      straightforward due to input format variation).
    - Drop build-time 2to3 invocation in favor of debian/patches/2to3.
  * debian/source/lintian-overrides: No more rapidjson10 (just ...11).
  * Standards-Version: 4.7.0 (routine-update)

 -- Aaron M. Ucko <ucko@debian.org>  Thu, 25 Jul 2024 20:07:36 -0400

ncbi-blast+ (2.12.0+ds-4) unstable; urgency=medium

  * debian/control: Drop build dependency on libpcre3-dev; PCRE2 support
    isn't ready yet, but there's a convenience copy of classic PCRE that
    will suffice for now.  (Partly addresses #891197.)
  * debian/source/lintian-overrides: Accommodate bracketed paths.
  * Standards-Version: 4.6.2 (routine-update)
  * Remove trailing whitespace in debian/changelog (routine-update)
  * Refer to common license file for Apache-2.0.
  * Avoid explicitly specifying -Wl,--as-needed linker flag.

 -- Aaron M. Ucko <ucko@debian.org>  Mon, 04 Sep 2023 22:40:42 -0400

ncbi-blast+ (2.12.0+ds-3) unstable; urgency=medium

  * d/patches/optin_usage_report change usage reports sending over
    internet strategy to optin (disabled by default unless specified)
    (Closes # 1005279).

 -- Olivier Sallou <osallou@debian.org>  Thu, 10 Feb 2022 12:17:56 +0000

ncbi-blast+ (2.12.0+ds-2) unstable; urgency=medium

  * Clean up spurious release-status comment from 2.12.0+ds-1.
  * debian/patches/system_mbedtls_only: Patch out use of local mbed TLS
    headers, which formally rename all symbols.

 -- Aaron M. Ucko <ucko@debian.org>  Wed, 01 Dec 2021 23:36:32 -0500

ncbi-blast+ (2.12.0+ds-1) unstable; urgency=medium

  * New upstream release.
  * debian/patches: Update accordingly.
    - fix_lib_deps, fix_unit_tests, spelling: Formally refresh to eliminate
      fuzz.
    - fix_x86isms: Retire (fully incorporated upstream.)
    - run_perl_directly: Formally update to reflect current $Id$ comment.
    - support_x32: Forward-port.
    - tune_lmdb_defaults: Keep just the MIPS tuneup; upstream's settings
      should now be fine elsewhere.
  * Standards-Version: 4.6.0 (routine-update)
  * watch file standard 4 (routine-update)
  * debian/patches/suppress_tls_version_checks (formerly
    suppress_gnutls_version_check): Suppress the mbed TLS version check too.
    (Closes: #1000358.)
  * debian/watch: Correct filenamemangle (wrong syntax for multiple rules,
    and leading components left unstripped).
  * debian/source/lintian-overrides: Simplify c++/src/html/ncbi_menu*.js
    overrides per current Lintian.

 -- Aaron M. Ucko <ucko@debian.org>  Wed, 01 Dec 2021 22:27:15 -0500

ncbi-blast+ (2.11.0+ds-1) unstable; urgency=medium

  [ Steffen Möller ]
  * Update metadata - fixed indenting.

  [ Aaron M. Ucko ]
  * New upstream release.
  * debian/patches: Update accordingly.
    - bm-6.4.0: Retire (fully incorporated upstream).
    - fix_lib_deps: Formally refresh to eliminate fuzz.
    - run_perl_directly: Formally update to reflect current $Id$ comment.
    - tune_lmdb_defaults: Port to new setup, conveniently macro-driven.
  * Standards-Version: 4.5.1 (routine-update)
  * debhelper-compat 13 (routine-update)

 -- Aaron M. Ucko <ucko@debian.org>  Sun, 31 Jan 2021 21:23:21 -0500

ncbi-blast+ (2.10.1+ds-1) unstable; urgency=medium

  * Repack without c++/src/build-system/project_tree_builder_gui/bin.
    Debian builds make no use of this (Java) GUI or supporting third-party
    jars, and could do without prebuilt binaries even if they did use it.
  * debian/copyright:
    - Set Files-Excluded accordingly.
    - Correct typos for c++/src/html/ncbi_menu*.js; in particular, replace
      duplicate .../ncbi_menu_dnd.js by .../ncbi_menu_dyn.js.
  * debian/watch: Set dversionmangle and repacksuffix options accordingly.
  * debian/source/lintian-overrides: For ncbi_menu*.js, which are editable
    despite long lines, override source-contains-prebuilt-javascript-object
    in addition to source-is-missing.

 -- Aaron M. Ucko <ucko@debian.org>  Fri, 23 Oct 2020 17:23:46 -0400

ncbi-blast+ (2.10.1-3) unstable; urgency=medium

  * debian/patches/tune_lmdb_defaults: Scale down slightly more on 32-bit
    mips* (just mipsel in practice these days).  The sizes at this point
    are 640 MiB there, 750 MB on other 32-bit platforms, and 20 GB on
    64-bit platforms.

 -- Aaron M. Ucko <ucko@debian.org>  Sun, 04 Oct 2020 21:37:04 -0400

ncbi-blast+ (2.10.1-2) unstable; urgency=medium

  * debian/patches/bm-6.4.0 (new): Update embedded copy of BitMagic to
    version 6,4.0 (from 6.0.0), addressing new "inlining failed in call to
    'always_inline'" errors on mips*el.  (The bmagic package currently has
    version 6.3.0, slightly predating the necessary fix.)

 -- Aaron M. Ucko <ucko@debian.org>  Sun, 20 Sep 2020 21:30:04 -0400

ncbi-blast+ (2.10.1-1) unstable; urgency=medium

  * New upstream release.
    - Among other changes, "fix tblastn mt issue".  (Closes: #970344.)
  * debian/patches/fix_x86isms (new): Conditionally stub out
    CCpuFeatures::InstructionSet::InstructionSet, which compiles only on x86.
  * debian/patches/{hurd_fixes,run_perl_directly}: Rebase.
  * debian/patches/{reprobuild,support_x32}: Refresh (had fuzz).
  * debian/patches/support_gcc10: Drop build-system portions, incorporated
    upstream as of this release.
  * debian/patches/tune_lmdb_defaults: Rename from tune_32bit_lmdb_defaults;
    scale down somewhat even on 64-bit platforms to account for potential
    use of qemu.  (Closes: #969608.)

 -- Aaron M. Ucko <ucko@debian.org>  Sat, 19 Sep 2020 22:45:42 -0400

ncbi-blast+ (2.10.0-3) unstable; urgency=medium

  * debian/patches/tune_32bit_lmdb_defaults: Tweak default map size expressions.
    - For 64-bit platforms, use an explicit UL suffix on one factor to avoid
      overflow.
    - For 32-bit platforms, avoid tying up quite so much address space, since
      opening a pair of databases is a distinct possibility.
    - Generally parenthesize expressions per best macro practice.

 -- Aaron M. Ucko <ucko@debian.org>  Mon, 07 Sep 2020 21:15:02 -0400

ncbi-blast+ (2.10.0-2) unstable; urgency=high

  * debian/patches/support_gcc10: Additionally tweak ncbifile.cpp to avoid
    narrowing errors on some platforms (i386, for one).
  * debian/patches/tune_32bit_lmdb_defaults (new): Conditionalize default
    map size to avoid allocation failures on 32-bit platforms.
    (Closes: #969608.)

 -- Aaron M. Ucko <ucko@debian.org>  Sun, 06 Sep 2020 23:07:37 -0400

ncbi-blast+ (2.10.0-1) unstable; urgency=medium

  * New upstream release.
  * debian/patches:
    - Formally refresh.  (A few files needed straightforward manual
      intervention.)
    - support_gcc10: New, for formal support of GCC 10+.  (Closes: #957581.)
    - run_perl_directly: New, to streamline update_blastdb(.pl)'s #! line.
  * debian/rules:
    - override_dh_clean: Clean up new generated artifacts: fakehome/ and
      c++/include/common/ncbi_revision.h.
    - override_dh_install-arch: Install new cleanup-blastdb-volumes script
      without its upstream .py suffix.
    - Stop directly injecting -Wl,--as-needed into LDFLAGS, but keep
      DEB_LDFLAGS_MAINT_APPEND for the sake of backports, along with a
      comment that they can't rely on GCC 9+.
  * Add salsa-ci file (routine-update)
  * Wrap long lines in changelog entries: 2.2.25-6.

 -- Aaron M. Ucko <ucko@debian.org>  Sun, 26 Apr 2020 19:38:13 -0400

ncbi-blast+ (2.9.0-4) unstable; urgency=high

  * debian/control: Standards-Version: 4.5.0 (already compliant).
  * debian/rules: DEB_CONFIGURE_COMMON_FLAGS += --without-sse42.
    (Closes: #951280.)

 -- Aaron M. Ucko <ucko@debian.org>  Sun, 16 Feb 2020 20:16:33 -0500

ncbi-blast+ (2.9.0-3) unstable; urgency=medium

  * Team upload.
  * Drop transitional blast2 package. (Closes: #940742).
  * debian/copyright: refreshed
  * debhelper-compat 12
  * Secure URI in copyright format
  * Remove trailing whitespace in debian/changelog
  * Use secure URI in Homepage field.
  * Move source package lintian overrides to debian/source.
  * Set upstream metadata fields: Contact, Name.
  * Remove obsolete fields Name, Contact from debian/upstream/metadata.

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Thu, 05 Dec 2019 15:42:44 +0100

ncbi-blast+ (2.9.0-2) unstable; urgency=medium

  * debian/control: Standards-Version: 4.4.1 (already compliant).
  * debian/copyright: Remove redundant ncbi_menu_*.js stanza.
  * debian/rules:
    - Delegate dpkg-{architecture,buildflags} calls to
      /usr/share/dpkg/{architecture,buildflags}.mk respectively.
    - Allow for cross-building (Closes: #930240):
    -- Factor a DEB_CONFIGURE_COMMON_FLAGS macro out of
       DEB_CONFIGURE_EXTRA_FLAGS for flags that also make sense for native
       builds of internal helpers.
    -- Conditionally supply --build=... and --host= to the main
       (historically, only) configure run per Helmut Grohne's suggestion.
       (dh_auto_configure would take care of this, but insists on passing
       a --runstatedir=... flag this configure script doesn't accept.)
    -- Conditionally add a rule for building native datatool and
       project_tree_builder binaries (in a parallel build tree established
       via another configure invocation), make it a dependency of
       override_dh_auto_configure-arch, and arrange for everything else to
       use these binaries as needed.
    -- Honor DEB_BUILD_OPTIONS="... nocheck ...", also per Helmut.
    -- Rework logic to install (possibly indirect) local library
       dependencies to use readelf rather than ldd, making as many passes
       as necessary (four at present, but no hardcoded count).
    - Install get_species_taxids without the .sh suffix.

 -- Aaron M. Ucko <ucko@debian.org>  Sun, 29 Sep 2019 21:57:31 -0400

ncbi-blast+ (2.9.0-1) unstable; urgency=medium

  * New upstream release

 -- Olivier Sallou <osallou@debian.org>  Wed, 11 Sep 2019 07:44:38 +0000

ncbi-blast+ (2.8.1-2) unstable; urgency=medium

  * Convert windowmasker_2.2.22_adapter to Python 3 via 2to3;
    update (build-)dependencies accordingly.  (Closes: #937121.)

 -- Aaron M. Ucko <ucko@debian.org>  Sun, 01 Sep 2019 20:50:43 -0400

# Older entries have been removed from this changelog.
# To read the complete changelog use `apt changelog ncbi-blast+`.
