[med-svn] [Git][med-team/ncbi-blastplus][master] 5 commits: + debian/patches/fix_bm_for_gcc15 (#1097434).
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Sun May 4 04:51:48 BST 2025
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-blastplus
Commits:
45fd0e43 by Aaron M. Ucko at 2025-05-03T22:16:45-04:00
+ debian/patches/fix_bm_for_gcc15 (#1097434).
Cherry-pick a BitMagic fix needed for modern compilers, adjusting the
path appropriately.
- - - - -
95db9968 by Aaron M. Ucko at 2025-05-03T22:20:25-04:00
Build against VDB where available (amd64/arm64/x32) (#1100037).
* debian/control: Build-depend on libncbi-vdb-dev where available.
* debian/rules: Build against (packaged!) VDB where available, using
logic cribbed from ncbi-igblast.
- - - - -
fafbce9e by Aaron M. Ucko at 2025-05-03T22:21:56-04:00
Standards-Version: 4.7.2 (routine-update)
- - - - -
1e3d4db4 by Aaron M. Ucko at 2025-05-03T23:49:21-04:00
debian/copyright: Overhaul with much help from licenserecon (lrc).
- - - - -
77af51e3 by Aaron M. Ucko at 2025-05-03T23:49:21-04:00
Finalize ncbi-blast+ 2.16.0+ds-7 for unstable.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/fix_bm_for_gcc15
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+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 at 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
=====================================
debian/control
=====================================
@@ -13,6 +13,7 @@ Build-Depends-Arch: libboost-test-dev,
libgnutls28-dev,
liblmdb-dev,
libmbedtls-dev,
+ libncbi-vdb-dev [amd64 arm64 x32],
libnghttp2-dev,
libpcre2-dev,
libsqlite3-dev,
@@ -20,7 +21,7 @@ Build-Depends-Arch: libboost-test-dev,
time,
zlib1g-dev,
procps
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/ncbi-blastplus
Vcs-Git: https://salsa.debian.org/med-team/ncbi-blastplus.git
Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
=====================================
debian/copyright
=====================================
@@ -5,7 +5,7 @@ Files-Excluded: c++/src/build-system/project_tree_builder_gui/bin
Files: c++/*
Copyright: NCBI
-License: PD
+License: public-domain
PUBLIC DOMAIN NOTICE
National Center for Biotechnology Information
.
@@ -27,7 +27,9 @@ License: PD
Please cite the author in any work or product based on this material.
Files: c++/src/connect/mbedtls/*
-Copyright: 2006-2015, ARM Limited, All Rights Reserved
+Copyright: 2006-2024, The Mbed TLS Contributors
+License: Apache-2.0
+
License: Apache-2.0
Licensed under the Apache License, Version 2.0 (the "License"); you may
not use this file except in compliance with the License.
@@ -56,7 +58,7 @@ License: Netscape
Files: c++/*/util/compress/zlib/*
Copyright: 1995-2004 Jean-loup Gailly and Mark Adler
-License: BSD-3-clause
+License: Zlib
This software is provided 'as-is', without any express or implied
warranty. In no event will the authors be held liable for any damages
arising from the use of this software.
@@ -74,9 +76,42 @@ License: BSD-3-clause
3. This notice may not be removed or altered from any source distribution.
Files: c++/*/util/regexp/*
-Copyright: 1997-2009 University of Cambridge
- 2008-2009 Google Inc
-License: BSD-4-clause
+Copyright: 1997-2018 University of Cambridge
+ 2009-2018 Zoltan Herczeg
+ 2005-2012 Google Inc
+License: BSD-3-clause
+
+Files: c++/*/util/regexp/ctre/*
+Copyright: 2023 Hana Dusíková
+License: Apache-2.0
+
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ * Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ .
+ * Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ .
+ * Neither the name of the University of Cambridge nor the name of Google
+ Inc. nor the names of their contributors may be used to endorse or
+ promote products derived from this software without specific prior
+ written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ POSSIBILITY OF SUCH DAMAGE.
Files: c++/*/util/compress/bzip2/*
Copyright: 1996-2002 Julian R Seward
@@ -114,9 +149,20 @@ Files: c++/src/build-system/config.*s*
Copyright: 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003 Free Software Foundation, Inc
License: GPL-2
+Files: c++/src/build-system/m4/ax_check_gnu_make.m4
+Copyright: 2008 John Darrington <j.darrington at elvis.murdoch.edu.au>
+ 2015 Enrico M. Crisostomo <enrico.m.crisostomo at gmail.com>
+License: FSFAP
+
Files: c++/src/build-system/m4/ax_jni_include_dir.m4
Copyright: 2008 Don Anderson <dda at sleepycat.com>
-License: as_is
+License: FSFAP
+
+Files: c++/src/build-system/m4/ax_prog_cc_for_build.m4
+Copyright: 2008 Paolo Bonzini <bonzini at gnu.org>
+License: FSFAP
+
+License: FSFAP
Copying and distribution of this file, with or without modification, are
permitted in any medium without royalty provided the copyright notice
and this notice are preserved. This file is offered as-is, without any
@@ -147,9 +193,21 @@ License: Boost
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
-Files: c++/include/dbapi/driver/odbc/unix_odbc/sqlfront.h
+Files: c++/include/dbapi/driver/odbc/unix_odbc/*.h
Copyright: 1998-1999 Brian Bruns
-License: GPL-2
+License: LGPL-2+
+ This library is free software; you can redistribute it and/or modify
+ it under the terms of the GNU Library General Public License as
+ published by the Free Software Foundation; either version 2 of the
+ License, or (at your option) any later version.
+ .
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Library General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, see https://www.gnu.org/licenses/.
License: GPL-2
This package is free software; you can redistribute it and/or modify
@@ -170,29 +228,191 @@ License: GPL-2
Files: c++/include/util/bitset/*
-Copyright: 2002-2003 Anatoliy Kuznetsov
-License: MIT
- Permission is hereby granted, free of charge, to any person
- obtaining a copy of this software and associated documentation
- files (the "Software"), to deal in the Software without restriction,
- including without limitation the rights to use, copy, modify, merge,
- publish, distribute, sublicense, and/or sell copies of the Software,
- and to permit persons to whom the Software is furnished to do so,
- subject to the following conditions:
- The above copyright notice and this permission notice shall be included
- in all copies or substantial portions of the Software.
+Copyright: 2002-2012 Anatoliy Kuznetsov
+License: Apache-2.0
+
+Files: c++/include/util/bitset/sse2neon.h
+Copyright: 2021 Distributed Ledger Technology collaboration
+License: Expat
+
+Files: c++/include/corelib/hash_impl/*
+Copyright: 1994 Hewlett Packard Company
+ 1996-1998 Silicon Graphics Computer Systems, Inc.
+License: NTP
+ Permission to use, copy, modify, distribute and sell this software
+ and its documentation for any purpose is hereby granted without fee,
+ provided that the above copyright notice appear in all copies and
+ that both that copyright notice and this permission notice appear
+ in supporting documentation. Silicon Graphics makes no
+ representations about the suitability of this software for any
+ purpose. It is provided "as is" without express or implied warranty.
+
+
+Files: c++/*/corelib/teamcity_*
+Copyright: 2011 JetBrains s.r.o.
+License: Apache-2.0
+
+
+Files: c++/include/misc/jsonwrapp/rapidjson*/*
+Copyright: 2015 THL A29 Limited, a Tencent company, and Milo Yip.
+License: Expat
+
+Files: c++/include/misc/jsonwrapp/rapidjson*/msinttypes/*
+Copyright: 2006-2013 Alexander Chemeris
+License: BSD-3-Clause
+
+Files: c++/include/objtools/blast/seqdb_reader/impl/lmdb++.h c++/*/util/lmdbxx/*
+Copyright: 2015 Arto Bendiken <argo at bendiken.net>
+License: Unlicense
+ This is free and unencumbered software released into the public domain.
+ .
+ Anyone is free to copy, modify, publish, use, compile, sell, or
+ distribute this software, either in source code form or as a compiled
+ binary, for any purpose, commercial or non-commercial, and by any
+ means.
+ .
+ In jurisdictions that recognize copyright laws, the author or authors
+ of this software dedicate any and all copyright interest in the
+ software to the public domain. We make this dedication for the benefit
+ of the public at large and to the detriment of our heirs and
+ successors. We intend this dedication to be an overt act of
+ relinquishment in perpetuity of all present and future rights to this
+ software under copyright law.
.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
- IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
- DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+ OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
OTHER DEALINGS IN THE SOFTWARE.
+ .
+ For more information, please refer to <http://unlicense.org/>
+
+Files: c++/include/util/timsort.hpp
+Copyright: 2011 Goro Fuji <gfuji at cpan.org>
+License: Expat
+
+License: Expat
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+Files: c++/src/algo/blast/core/boost_erf.c
+Copyright: 2006 John Maddock
+License: BSL-1.0
+ Boost Software License - Version 1.0 - August 17th, 2003
+ .
+ Permission is hereby granted, free of charge, to any person or
+ organization obtaining a copy of the software and accompanying
+ documentation covered by this license (the "Software") to use,
+ reproduce, display, distribute, execute, and transmit the
+ Software, and to prepare derivative works of the Software, and
+ to permit third-parties to whom the Software is furnished to do
+ so, all subject to the following:
+ .
+ The copyright notices in the Software and this entire statement,
+ including the above license grant, this restriction and the
+ following disclaimer, must be included in all copies of the
+ Software, in whole or in part, and all derivative works of the
+ Software, unless such copies or derivative works are solely in
+ the form of machine-executable object code generated by a source
+ language processor.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND
+ NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR
+ ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR
+ OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ OTHER DEALINGS IN THE SOFTWARE.
+
+Files: c++/src/build-system/cmake/unused/FindPCRE.cmake
+Copyright: 2011 Martin Konrad <konrad at ikp.tu-darmstadt.de>
+License: GPL-2+
+
+Files: c++/src/build-system/cmake/unused/HunterGate.cmake
+Copyright: 2013-2017 Ruslan Baratov
+License: BSD-2-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ * Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+ .
+ * Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Files: c++/src/build-system/configure
+Copyright: 1992-1996, 1998-2012 Free Software Foundation, Inc.
+License: FSFUL
+ This configure script is free software; the Free Software Foundation
+ gives unlimited permission to copy, distribute and modify it.
+
+Files: c++/src/connect/parson.*
+Copyright: 2012-2016 Krzysztof Gabis
+License: Expat
+
+Files: c++/src/util/checksum/????hash/*
+Copyright: 2011 Google, Inc.
+License: Expat
+
+Files: c++/src/util/compress/api/miniz/*
+Copyright: 2013-2014 RAD Game Tools and Valve Software
+ 2010-2014 Rich Geldreich and Tenacious Software LLC
+License: Expat
+
+Files: c++/*/util/lmdb/*
+Copyright: 2011-2019 Howard Chu, Symas Corp.
+ 2009, 2010 Martin Hedenfalk <martin at bzero.se>
+License: OLDAP-2.8
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted only as authorized by the OpenLDAP
+ Public License.
+ .
+ A copy of this license is available in the file LICENSE in
+ c++/src/util/lmdb or, alternatively, at
+ <http://www.OpenLDAP.org/license.html>.
Files: debian/*
-Copyright: 2011 Olivier Sallou <olivier.sallou at irisa.fr>
+Copyright: 2011-2016, 2018-2021, 2023-2025 Aaron M. Ucko <ucko at debian.org>
+ 2011, 2012, 2015, 2016, 2020 Andreas Tille <tille at debian.org>
+ 2018 David Miguel Susano Pinto <carandraug+dev at gmail.com>
+ 2020 Iain Lane <iain at orangesquash.org.uk>
+ 2019 Michael R. Crusoe <michael.crusoe at gmail.com>
+ 2011-2019, 2022 Olivier Sallou <olivier.sallou at irisa.fr>
+ 2010, 2018-2020 Steffen Möller <moeller at debian.org>
+ 2011 Tim Booth <tbooth at ech.ac.uk>
+ 2016 Canberk Koç <canberkkoc at gmail.com>
+License: GPL-2+
+
License: GPL-2+
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
=====================================
debian/patches/fix_bm_for_gcc15
=====================================
@@ -0,0 +1,31 @@
+From fab01f43eca266bf56efb1aca659773c911a83fb Mon Sep 17 00:00:00 2001
+From: Anatoliy Kuznetsov <anatoliy.kuznetsov at gmail.com>
+Date: Tue, 3 Sep 2024 15:29:08 -0400
+Subject: [PATCH] fixed clang compilation issues
+
+---
+ c++/include/util/bitset/bm.h | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/c++/include/util/bitset/bm.h b/c++/include/util/bitset/bm.h
+index 70996e53..05bb139c 100644
+--- a/c++/include/util/bitset/bm.h
++++ b/c++/include/util/bitset/bm.h
+@@ -523,7 +523,7 @@ class bvector
+ {
+ bvect_ = ii.bvect_;
+ if (!buf_)
+- buf_ = bvect_->allocate_tempblock();
++ buf_ = (value_type*) bvect_->blockman_.get_allocator().alloc_bit_block();
+ buf_size_ = ii.buf_size_;
+ ::memcpy(buf_, ii.buf_, buf_size_ * sizeof(*buf_));
+ sorted_ = ii.sorted_;
+@@ -534,7 +534,7 @@ class bvector
+ {
+ bvect_ = ii.bvect_;
+ if (buf_)
+- bvect_->free_tempblock(buf_);
++ bvect_->blockman_.get_allocator().free_bit_block((bm::word_t*)buf_);
+ buf_ = ii.buf_; ii.buf_ = 0;
+ buf_size_ = ii.buf_size_;
+ sorted_ = ii.sorted_;
=====================================
debian/patches/series
=====================================
@@ -21,3 +21,4 @@ run_perl_directly
tune_lmdb_defaults
2to3
big_endian_workaround
+fix_bm_for_gcc15
=====================================
debian/rules
=====================================
@@ -17,11 +17,21 @@ endif
DEB_CONFIGURE_COMMON_FLAGS=--without-autodep --without-makefile-auto-update \
--with-flat-makefile --without-caution --without-dbapi --without-lzo \
- --without-debug --without-downloaded-vdb --without-sse42
+ --without-debug --without-sse42
DEB_CONFIGURE_EXTRA_FLAGS=$(DEB_CONFIGURE_COMMON_FLAGS) --with-dll --with-mt \
--with-runpath=/usr/lib/ncbi-blast+ --with-build-root=BUILD \
--with-mbedtls --with-pcre2
+ifneq (,$(filter amd64 arm64 x32,$(DEB_HOST_ARCH)))
+ VDB_SUBTREES=os/$(DEB_HOST_ARCH_OS) os/unix cc/gcc/$(DEB_HOST_GNU_CPU) cc/gcc
+ VDB_INC=-I/usr/include/ncbi-vdb
+ VDB_INCLUDE=$(VDB_INC) $(VDB_SUBTREES:%=$(VDB_INC)/%)
+ DEB_CONFIGURE_COMMON_FLAGS += --with-vdb=/usr VDB_INCLUDE="$(VDB_INCLUDE)"
+else
+ DEB_CONFIGURE_COMMON_FLAGS += --without-downloaded-vdb
+endif
+
+
proj=algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/
#ifneq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/5f9892c67b474913eaf0d9b5f9261a8d771dbd28...77af51e35721ccda06cd4a16fd1a3497a4a217f4
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/5f9892c67b474913eaf0d9b5f9261a8d771dbd28...77af51e35721ccda06cd4a16fd1a3497a4a217f4
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