--- /dev/null
++ncbi-blast+ (2.8.1-1) UNRELEASED; urgency=medium
++
++ * New upstream release (NOT RELEASED YET).
++
++ -- Aaron M. Ucko <ucko@debian.org> Sun, 03 Feb 2019 10:38:33 -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