--- /dev/null
- ncbi-blast+ (2.15.0+ds-1) UNRELEASED; urgency=medium
++ncbi-blast+ (2.16.0+ds-1) UNRELEASED; urgency=medium
+
+ * New upstream release, which should be (more than) new enough for
+ recent q2-feature-classifier. (Closes: #1074316.) (NOT RELEASED YET.)
+ * 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).
+
- -- Aaron M. Ucko <ucko@debian.org> Thu, 25 Jul 2024 20:00:49 -0400
++ -- Aaron M. Ucko <ucko@debian.org> Thu, 25 Jul 2024 20:02:37 -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
+
+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
projects / ncbi-blast+.git / commitdiff