ncbi-blast+ (2.12.0+ds-4build2) noble; urgency=medium

  * No-change rebuild for CVE-2024-3094

 -- William Grant <wgrant@ubuntu.com>  Mon, 01 Apr 2024 18:01:27 +1100

ncbi-blast+ (2.12.0+ds-4build1) noble; urgency=medium

  * No-change rebuild against libmbedcrypto7t64

 -- Steve Langasek <steve.langasek@ubuntu.com>  Sun, 17 Mar 2024 18:09:58 +0000

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

ncbi-blast+ (2.8.1-1) unstable; urgency=medium

  * New upstream release.
  * debian/compat: Advance to Debhelper 11.
  * debian/control:
    - Build-Depend on liblmdb-dev.
    - Split B-Ds other than Debhelper out to Build-Depends-Arch.
    - Advance Debhelper requirement to 11~.
    - Standards-Version: 4.3.0 (already compliant).
    - Rules-Requires-Root: no.
  * debian/patches: Formally update for new release.
    - Retire support_boost_1_67 (already applied upstream).
    - Update patches that apply with offsets or outright fuzz, or need
      full-fledged porting.
  * debian/patches/fix_lib_deps: Link xcleanup against $(OBJEDIT_LIBS).
  * debian/patches/system_mbedtls_only (new): Omit convenience mbed TLS
    copy, which is dead weight and yielded a Lintian error.
  * debian/rules: Also skip (dh_auto)_configure when building only
    architecture-independent binary packages.

 -- Aaron M. Ucko <ucko@debian.org>  Sun, 03 Feb 2019 22:47:45 -0500

ncbi-blast+ (2.7.1-2) unstable; urgency=medium

  [ David Miguel Susano Pinto ]
  * d/control: fix Vcs-* links to point to salsa

  [ Aaron M. Ucko ]
  * d/control: Standards-Version: 4.2.1 (already compliant).
  * d/patches/support_boost_1_67: New patch to extend Boost support
    (used for uninstalled tests) through at least version 1.67, per
    upstream (https://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/c%2B%2B)
    revisions 79910, 79926, 79928, and 79929.  (Closes: #916000.)

 -- Aaron M. Ucko <ucko@debian.org>  Wed, 12 Dec 2018 22:24:45 -0500

ncbi-blast+ (2.7.1-1) unstable; urgency=medium

  * New upstream release
    d/patches: update patch for new release
    d/control:
      go to standards 4.1.3
      add mbedtls dependency

 -- Olivier Sallou <osallou@debian.org>  Sat, 10 Feb 2018 17:35:31 +0000

ncbi-blast+ (2.6.0-1) unstable; urgency=medium

  * New upstream release

 -- Olivier Sallou <osallou@debian.org>  Sun, 15 Jan 2017 17:12:27 +0000

ncbi-blast+ (2.5.0-4) unstable; urgency=medium

  * New optionally_keep_sequence patch to hang on to sequence data even if
    -parse_deflines recognized a non-local ID, on the condition that the
    environment variable BLAST_ALWAYS_KEEP_SEQUENCE (or configuration
    parameter [BLAST] always_keep_sequence) is set to a "true" value
    (English-only, case-insensitive true, t, yes, y, or 1).  (Closes: #792510.)

 -- Aaron M. Ucko <ucko@debian.org>  Wed, 14 Dec 2016 22:46:44 -0500

ncbi-blast+ (2.5.0-3) unstable; urgency=medium

  * New suppress_gnutls_version_check patch to prevent bailing when the
    exact compile-time and runtime GNU TLS versions differ; trust dpkg to
    disallow combinations that are actually incompatible.
  * debian/rules: If configure fails (as has been happening on alpha),
    present (BUILD/status/)config.log before bailing.

 -- Aaron M. Ucko <ucko@debian.org>  Wed, 07 Dec 2016 21:40:38 -0500

ncbi-blast+ (2.5.0-2) unstable; urgency=medium

  * debian/patches/fix_lib_deps: Patch Makefile.blast_macros.mk to add blast
    to BLAST_LIBS to clear up link errors that could otherwise occur.
  * debian/control: B-D on libgnutls28-dev to enable HTTPS support.
  * Fully take blast2 over from ncbi-tools6, whose implementation has retired.

 -- Aaron M. Ucko <ucko@debian.org>  Mon, 05 Dec 2016 23:16:54 -0500

ncbi-blast+ (2.5.0-1) unstable; urgency=medium

  * New upstream release

 -- Olivier Sallou <osallou@debian.org>  Thu, 01 Dec 2016 14:40:17 +0100

ncbi-blast+ (2.4.0-3) unstable; urgency=medium

  * debian/rules:
    - Properly build (but don't install) run_with_lock. (Closes: #833538.)
    - Comment out nostrip check, which yielded a useless dbgsym package.
  * Reinstate and refresh the hurd_fixes patch, which mostly still applies.
    (Closes: #833539.)
  * Add a new support_x32 patch to avoid picking up wrong inline assembly.
    (Closes: #833541.)

 -- Aaron M. Ucko <ucko@debian.org>  Fri, 05 Aug 2016 19:47:24 -0400

ncbi-blast+ (2.4.0-2) unstable; urgency=medium

  * Import upstream patch for remaining Boost compatibility issues
    as debian/patches/support_recent_boost.  (Closes: #833451.)
  * debian/rules: Automatically determine which libraries are needed.
    (The hand-maintained blacklist was incomplete.)

 -- Aaron M. Ucko <ucko@debian.org>  Thu, 04 Aug 2016 23:08:20 -0400

ncbi-blast+ (2.4.0-1) unstable; urgency=medium

  * New upstream release.
  * Refresh patches; drop fix_kfreebsd_ftbs.patch (applied upstream).
  * Import upstream patch to fix Boost version detection (which missed the
    2.4.0 release branch) as debian/patches/fix_version_extraction.
  * fix_lib_deps: List taxon1 in align_format's overridden DLL_LIB, in
    large part to ensure its headers are generated on time; generally fix
    remaining cases of underlinkage (several longstanding).
  * debian/rules: Build --without-downloaded-vdb, to avoid trying to go to
    Github for code that BLAST+ doesn't even use.  (Other parts of the C++
    Toolkit do.)
  * debian/control: Go ahead and add myself to Uploaders.

 -- Aaron M. Ucko <ucko@debian.org>  Wed, 03 Aug 2016 21:40:00 -0400

ncbi-blast+ (2.3.0-2) unstable; urgency=medium

  * Team upload.
  * Autopkgtest added

 -- Canberk Koç <canberkkoc@gmail.com>  Tue, 02 Aug 2016 03:32:09 +0300

ncbi-blast+ (2.3.0-1) unstable; urgency=medium

  * New upstream version
  * Moved packaging to Git
  * cme fix dpkg-control
  * drop get-orig-source target which is simply the usual uscan call

 -- Andreas Tille <tille@debian.org>  Tue, 12 Apr 2016 14:54:08 +0200

ncbi-blast+ (2.2.31-4) unstable; urgency=medium

  * Really enable building architecture independent package separately
    Closes: #809120
  * Save time and do nothing for architecture independent builds

 -- Andreas Tille <tille@debian.org>  Thu, 07 Jan 2016 18:50:31 +0100

ncbi-blast+ (2.2.31-3) unstable; urgency=medium

  * Drop explicite mentioning of quilt
  * Enable building architecture independent package separately
    Closes: #809120
  * Override false lintian error
  * DEP5 fixes

 -- Andreas Tille <tille@debian.org>  Mon, 28 Dec 2015 12:32:23 +0100

ncbi-blast+ (2.2.31-2) unstable; urgency=medium

  * Fix a long-standing typo for GNU/kFreeBSD FTBS (Aaron M. Ucko)

 -- Olivier Sallou <osallou@debian.org>  Fri, 11 Dec 2015 09:44:43 +0100

ncbi-blast+ (2.2.31-1) unstable; urgency=medium

  * New upstream release
  * Allow parallel build (Closes: #798277). Thanks to Aron Xu <aron@debian.org>
  * GCC break fix (recompile with gcc5, Closes: #793263).

 -- Olivier Sallou <osallou@debian.org>  Thu, 10 Dec 2015 13:37:03 +0100

ncbi-blast+ (2.2.30-4) unstable; urgency=medium

  * d/patches/fix_compilation: Add an upstream patch to
    include/util/bitset/bmconst.h to fix builds with GCC 5 on platforms
    such as arm64 on which char is unsigned.  (Closes: #790667.)

 -- Aaron M. Ucko <ucko@debian.org>  Thu, 02 Jul 2015 16:22:39 -0400

ncbi-blast+ (2.2.30-3) unstable; urgency=medium

  * Switch to unstable after unfreeze.

 -- Olivier Sallou <osallou@debian.org>  Mon, 18 May 2015 14:34:50 +0200

ncbi-blast+ (2.2.30-2) experimental; urgency=medium

  * d/patches/allow_gcc5 (new): Allow compilation with GCC 5, per upstream.
    (Closes: #778021.)

 -- Aaron M. Ucko <ucko@debian.org>  Mon, 16 Feb 2015 22:38:50 -0500

ncbi-blast+ (2.2.30-1) experimental; urgency=medium

  * New upstream release
  * d/control: switch to Standards 3.9.6
               fix svn url
  * d/patches/fix_compilation: fix compilation issue

 -- Olivier Sallou <osallou@debian.org>  Fri, 21 Nov 2014 18:21:26 +0100

ncbi-blast+ (2.2.29-3) unstable; urgency=medium

  * debian/patches/include_typeinfo: Patch include/corelib/ncbistl.hpp to
    ensure sufficient coverage; fix typos in patch headers.  (Closes: #753190.)
  * Standards-Version: 3.9.4.  (Already compliant.)

 -- Aaron M. Ucko <ucko@debian.org>  Tue, 01 Jul 2014 18:27:46 -0400

ncbi-blast+ (2.2.29-2) unstable; urgency=medium

  * d/patches/include_typeinfo (Closes: #753190).

 -- Olivier Sallou <osallou@debian.org>  Sat, 07 Jun 2014 11:28:22 +0200

ncbi-blast+ (2.2.29-1) unstable; urgency=medium

  * New upstream release

 -- Olivier Sallou <osallou@debian.org>  Fri, 06 Jun 2014 22:38:40 +0200

ncbi-blast+ (2.2.28-2) unstable; urgency=low

  * debian/patches/use_pie_for_apps: Explicitly build all executables with
    -fPIE -pie, to avoid giving project_tree_builder a partial PIE
    treatment that now fails on mips and mipsel.  (Closes: #710807.)
  * debian/rules: Retire redundant APP_LDFLAGS override.
  * Standards-Version: 3.9.4.  (Already compliant.)

 -- Aaron M. Ucko <ucko@debian.org>  Sun, 02 Jun 2013 23:00:44 -0400

ncbi-blast+ (2.2.28-1) unstable; urgency=low

  * New upstream release
    - Thanks to Tim Booth for package update help.

 -- Olivier Sallou <osallou@debian.org>  Sat, 01 Jun 2013 08:40:51 +0200

ncbi-blast+ (2.2.27-3) unstable; urgency=low

  * debian/series: active patch fix_arm_mips_build (Closes: #688661).

 -- Olivier Sallou <osallou@debian.org>  Fri, 05 Oct 2012 11:03:03 +0200

ncbi-blast+ (2.2.27-2) unstable; urgency=low

  * debian/patches/fix_arm_mips_build: Fix FTBS on ARM and MIPS
    (Closes: #688661).
  * debian/rules: rename seedtop to seedtop+ to avoid blast2 conflict
    (Closes: #688684).

 -- Olivier Sallou <osallou@debian.org>  Mon, 24 Sep 2012 09:28:29 +0200

ncbi-blast+ (2.2.27-1) unstable; urgency=low

  * New upstream release

 -- Olivier Sallou <osallou@debian.org>  Fri, 21 Sep 2012 17:25:41 +0200

ncbi-blast+ (2.2.26-3) unstable; urgency=low

  [ Aaron M. Ucko ]
  * debian/patches/fix_gcc47_errors: fix various GCC 4.7 compilation
    errors and warnings.  (Closes: #669679.)
    - Explicitly qualify more dependent names originating in base templates.
    - Directly #include headers as needed.
    - Use modern syntax for making protected base members public.
    - Add forward declarations as needed.
  * Wrap and sort build dependencies to ease maintenance thereof.
  * Enable full hardening flags, introducing a small patch
    (use_pie_for_apps) to reflect the need to build executables and
    libraries differently.
  * Use upstream's new --with-symbols flag in nostrip builds.

  [ Andreas Tille ]
  * debian/control: Modernize Vcs-* fields.

 -- Aaron M. Ucko <ucko@debian.org>  Thu, 10 May 2012 23:42:49 -0400

ncbi-blast+ (2.2.26-2) unstable; urgency=low

  * debian/patches/wrong_path_to_touch.patch :Fix upstream FTBFS on the Hurd
    hardcodes wrong path to touch (Closes: #663244)

 -- Olivier Sallou <osallou@debian.org>  Wed, 07 Mar 2012 17:29:23 +0100

ncbi-blast+ (2.2.26-1) unstable; urgency=low

  [ Olivier Sallou ]
  * New upstream release
  * Remove some patches, applied upstream

  [ Andreas Tille]
  * debian/copyright: Added Upstream-Contact

 -- Olivier Sallou <osallou@debian.org>  Wed, 07 Mar 2012 09:37:10 +0100

ncbi-blast+ (2.2.25-7) unstable; urgency=low

  * Do not output everything to STDERR in
    c++/src/app/blast/update_blastdb.pl
    Closes: #644237
  * debian/control: Depends s/${python:Depends}/python/ because
    the python dependency of /usr/bin/windowmasker_2.2.22_adapter
    is not detected obviosely
  * debian/copyright: Indentation fixes to get DEP5 compatibility

 -- Andreas Tille <tille@debian.org>  Wed, 21 Dec 2011 15:47:04 +0100

ncbi-blast+ (2.2.25-6) unstable; urgency=low

   * debian/control:
     + Luca Capello <luca@pca.it>, fix reference for legacy_blast
       (Closes: #642986).
     + add a new line to separate the actual description from usage
      instruction in the long Description:.
   * debian/rules: add gene_info_reader binary in package

 -- Olivier Sallou <olivier.sallou@irisa.fr>  Fri, 30 Sep 2011 12:31:05 -0400

ncbi-blast+ (2.2.25-5) unstable; urgency=low

  * Team upload.
  * debian/patches/hurd_fixes: further patch configure(.ac) to reflect
    -Wl,rpath,... support.  (Closes: #629656.)
  * debian/patches/fix_lib_deps: link makembindex and srsearch against
    libxconnect rather than libconnect for consistency with libblast,
    which uses the former for consistency with other projects.

 -- Aaron M. Ucko <ucko@debian.org>  Mon, 29 Aug 2011 12:31:05 -0400

ncbi-blast+ (2.2.25-4) unstable; urgency=low

  [ Aaron M. Ucko ]
  * Team upload.
  * debian/patches/support_other_cpus: belatedly add a descriptive header.
  * debian/patches/hurd_fixes: new; fix hurd-specific issues.
    (In conjunction with the following change, finally closes: #629656.)
  * debian/control:
    - Build-Depends += libc0.3-dev (>= 2.13-9~) [hurd-i386] to avoid #630180.
    - Declare both binary packages as Multi-Arch: foreign.
  * debian/patches/fix_lib_deps: new; ensure that all libraries link against
    all direct dependencies.  (Break the dependency loop between libxblast
    and libxalgoblastdbindex by having the former provide only the C++ BLAST
    API, leaving the C core only in libblast.)  (Closes: #633567.)
  * debian/rules: tweak LDFLAGS, supplying -Wl,--as-needed across the
    board (as it is now safe to do so) and adding -Wl,--enable-new-dtags
    to allow LD_LIBRARY_PATH to override the private rpath.
  * debian/patches/no_multiarch_rpath: new; avoid redundant rpath entries
    on multiarch systems (courtesy of overzealous logic to ensure
    executables will be able to find libstdc++.)

  [ Andreas Tille ]
  * Enhances: t-coffee (as stated in tasks file)

 -- Aaron M. Ucko <ucko@debian.org>  Sun, 28 Aug 2011 18:45:19 -0400

ncbi-blast+ (2.2.25-3) unstable; urgency=low

  * Team upload.
  * debian/rules:
    - Export MAKE to override an internal upstream build script that
      otherwise incorrectly defaults to gmake on non-Linux
      architectures. (Really closes: #629656, with any luck.)
    - Force CONFIG_SHELL=/bin/bash to avoid lossage that can occur with zsh4
      masquerading as ksh, which configure otherwise favors (due to complaints
      from users with broken BASH_ENV scripts that change directories).

 -- Aaron M. Ucko <ucko@debian.org>  Thu, 09 Jun 2011 19:25:45 -0400

ncbi-blast+ (2.2.25-2) unstable; urgency=low

  * Team upload.
  * Fix several sources of build failures (closes: #629656):
    - debian/rules (override_dh_install): Correctly support building only
      architecture-dependent packages.
      (DEB_CONFIGURE_EXTRA_FLAGS): Add --without-caution to override the
      upstream build system's reluctance to build shared libraries on the
      Hurd or kFreeBSD, which it doesn't specifically recognize.  Limit C++
      optimization level to -O (rather than the default -O2) on mips(el),
      on which g++ otherwise crashes. :-/
    - debian/patches/support_other_cpus (new; committed upstream too):
      build correctly on architectures that wound up defining
      NCBI_SLOW_ATOMIC_SWAP (spuriously in the case of powerpc,
      whose detection the patch fixes as well).

 -- Aaron M. Ucko <ucko@debian.org>  Wed, 08 Jun 2011 21:42:52 -0400

ncbi-blast+ (2.2.25-1) unstable; urgency=low

  * Initial release (Closes: #624394)

 -- Olivier Sallou <olivier.sallou@irisa.fr>  Wed, 08 Jun 2011 00:15:15 +0200
