debian/0000755000000000000000000000000012153003415007160 5ustar debian/compat0000644000000000000000000000000212152773066010375 0ustar 9 debian/watch0000644000000000000000000000030211570234561010216 0ustar version=3 opts=pasv,filenamemangle=s/\+-src/-orig/,filenamemangle=s/blast/blast+/ \ ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-(.*)\+-src\.tar\.gz debian uupdate debian/get-orig-source0000755000000000000000000000010111570234561012123 0ustar #!/bin/bash set -e uscan --rename --verbose --force-download debian/changelog0000644000000000000000000001526112153003334011037 0ustar 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 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 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 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 Mon, 24 Sep 2012 09:28:29 +0200 ncbi-blast+ (2.2.27-1) unstable; urgency=low * New upstream release -- Olivier Sallou 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 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 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 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 Wed, 21 Dec 2011 15:47:04 +0100 ncbi-blast+ (2.2.25-6) unstable; urgency=low * debian/control: Luca Capello , 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 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 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 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 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 Wed, 08 Jun 2011 21:42:52 -0400 ncbi-blast+ (2.2.25-1) unstable; urgency=low * Initial release (Closes: #624394) -- Olivier Sallou Wed, 08 Jun 2011 00:15:15 +0200 debian/rules0000755000000000000000000000626012152774716010266 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 DEB_CONFIGURE_EXTRA_FLAGS=--with-dll --with-mt --without-autodep \ --without-makefile-auto-update --with-flat-makefile --without-caution \ --without-dbapi --without-lzo --with-runpath=/usr/lib/ncbi-blast+ \ --with-build-root=BUILD --without-debug proj=algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/ ifneq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS))) DEB_CONFIGURE_EXTRA_FLAGS += --with-symbols endif #export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie export DEB_CFLAGS_MAINT_APPEND=-Wall -pedantic export DEB_LDFLAGS_MAINT_APPEND=-Wl,--as-needed DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH) CFLAGS := $(shell dpkg-buildflags --get CFLAGS) CPPFLAGS := $(shell dpkg-buildflags --get CPPFLAGS) CXXFLAGS := $(shell dpkg-buildflags --get CXXFLAGS) LDFLAGS := $(shell dpkg-buildflags --get LDFLAGS) -Wl,--as-needed ifneq (,$(findstring mips,$(DEB_HOST_ARCH))) CXXFLAGS := $(CXXFLAGS:-O%=-O) DEB_CONFIGURE_EXTRA_FLAGS += FAST_CXXFLAGS=-O endif export CFLAGS CPPFLAGS CXXFLAGS LDFLAGS MAKE llp=LD_LIBRARY_PATH override_dh_auto_configure: cd c++ && $(llp)=$(CURDIR)/c++/BUILD/lib$${$(llp)+:$$$(llp)} \ CONFIG_SHELL=/bin/bash ./configure $(DEB_CONFIGURE_EXTRA_FLAGS) override_dh_auto_build: cd c++/BUILD/build && \ make -f Makefile.flat all_projects="$(proj)" override_dh_auto_test: -dh_auto_test -c++/BUILD/build/check.sh concat_err -cat c++/BUILD/build/check.sh.out_err instroot = debian/ncbi-blast+/usr leg_bin = debian/ncbi-blast+-legacy/usr/share/ncbi-blast+/bin override_dh_auto_install: cp c++/BUILD/lib/*.so $(instroot)/lib/ncbi-blast+/ cp c++/BUILD/bin/* $(instroot)/bin/ override_dh_install: # dh_install mv $(instroot)/bin/rpsblast $(instroot)/bin/rpsblast+ mv $(instroot)/bin/seedtop $(instroot)/bin/seedtop+ mv $(instroot)/bin/legacy_blast.pl $(instroot)/bin/legacy_blast mv $(instroot)/bin/update_blastdb.pl $(instroot)/bin/update_blastdb mv $(instroot)/bin/windowmasker_2.2.22_adapter.py \ $(instroot)/bin/windowmasker_2.2.22_adapter # Clean up tests, demos, and internal build tools rm -f $(instroot)/bin/*test* $(instroot)/bin/seqdb_demo \ $(instroot)/bin/datatool \ $(instroot)/bin/project_tree_builder \ $(instroot)/lib/ncbi-blast+/libtest_*.so if test -d $(leg_bin); then cp debian/legacy/legacy.sh $(leg_bin)/; fi override_dh_clean: dh_clean #Tricky - for each module directory there may be several module files #or there may be none but then there is still a module named after the #directory. Clean everything! -for x in c++/src/objects/* ; do \ (cd "$$x" && ( \ mods="`echo *.module`" ; \ [ "$${mods#*\*}" = "$$mods" ] || mods="`basename $$x`" ; \ for mod in $$mods ; do \ ../../../BUILD/build/new_module.sh $$mod purge_sources ; \ done ) ; \ ) ; \ done rm -rf c++/compilers/dll c++/config.log c++/Makefile rm -f c++/configure.lineno c++/src/objects/blastxml/blastxml.module find -name check_exec.pid -delete rm -rf c++/BUILD %: dh $@ -Dc++ --with autotools_dev --with quilt get-orig-source: . debian/get-orig-source debian/README.source0000644000000000000000000000034012152773066011353 0ustar blast+ for Debian --------------------- get-orig-source target downloads file via uscan and rearrange the package. Patches are required for build. Lintian raises hardening no fortify warnings that are false positives. debian/ncbi-blast+-legacy.dirs0000644000000000000000000000003311570234561013404 0ustar /usr/share/ncbi-blast+/bin debian/control0000644000000000000000000000406112153003265010567 0ustar Source: ncbi-blast+ Section: science Priority: optional Build-Depends: autotools-dev (>= 20100122), debhelper (>= 9), dpkg-dev (>= 1.16.1), libboost-test-dev, libbz2-dev, libc0.3-dev (>= 2.13-9~) [hurd-i386], libpcre3-dev, quilt, time, zlib1g-dev Standards-Version: 3.9.4 Uploaders: Olivier Sallou , Andreas Tille Maintainer: Debian Med Packaging Team Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ncbi-blast+/trunk/ Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast+/trunk/ Package: ncbi-blast+ Architecture: any Enhances: t-coffee Depends: ncbi-data, python, ${misc:Depends}, ${perl:Depends}, ${shlibs:Depends} Multi-Arch: foreign Description: next generation suite of BLAST sequence search tools The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. There are versions of BLAST that compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as versions that translate nucleotide queries or databases in all six frames and compare to protein databases or queries. PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting with a protein query, and then uses that PSSM to perform further searches. It is also possible to compare a protein or nucleotide query to a database of PSSM’s. The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as a network service. Package: ncbi-blast+-legacy Architecture: all Depends: ncbi-blast+, ${misc:Depends} Multi-Arch: foreign Description: NCBI Blast legacy call script This package adds some fake scripts to call NCBI+ programs with the NCBI blast command line. It makes use of the legacy_blast script in ncbi-blast+ package. . To use those scripts, /usr/share/ncbi-blast+/bin must be added to the PATH. debian/copyright0000644000000000000000000002626711753103401011131 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: ncbi-blast+ Upstream-Contact: blastsoft@ncbi.nlm.nih.gov Files: c++/*/util/compress/zlib/* Copyright: 1995-2004 Jean-loup Gailly and Mark Adler License: 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. . Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: . 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 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 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 3. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 4. The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 AUTHOR 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 License: BSD Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 3. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 4. The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 AUTHOR 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/config.*s* c++/src/util/regexp/missing Copyright: 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003 Free Software Foundation, Inc 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 the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This package 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 General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". Files: c++/src/build-system/ax_jni_include_dir.m4 Copyright: 2008 Don Anderson License: 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 warranty. Files: c++/include/util/impl/floating_point_comparison.hpp Copyright: 2001-2008 Gennadiy Rozental License: Boost software license 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++/include/dbapi/driver/odbc/unix_odbc/sqlfront.h Copyright: 1998-1999 Brian Bruns 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 the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This package 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 General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". Files: c++/src/html/ncbi_menu_*.js Copyright: 1997-1999 Netscape Communications Corp. License: Netscape Netscape grants you a royalty free license to use or modify this software provided that this copyright notice appears on all copies. This software is provided "AS IS," without a warranty of any kind. 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. . 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++/* Copyright: NCBI License: PD PUBLIC DOMAIN NOTICE National Center for Biotechnology Information . This software/database is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the author's official duties as a United States Government employee and thus cannot be copyrighted. This software/database is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction. . Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose. . Please cite the author in any work or product based on this material. Files: debian/* Copyright: 2011 Olivier Sallou 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 the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This package 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 General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". debian/ncbi-blast+-legacy.links0000644000000000000000000000106611570234561013572 0ustar usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/blastall usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/megablast usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/blastpgp usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/bl2seq usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/rpsblast usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/fastacmd usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/formatdb usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/seedtop debian/README.Debian0000644000000000000000000000077011742121470011232 0ustar blast+ for Debian --------------------- This package does not include the documentation of the software. Documentation is available online. Detail is available: man ncbi-blast+ Package does not include test binaries nor datatool and projet_tree_builder from upstream. Those binaries are indeed for internal upstream use, and are of no use nor related to blast+ tool itself (see Bug #642991 discussion with upstream answers) -- Olivier Sallou Wed, 27 Apr 2011 15:19:59 +0200 debian/dirs0000644000000000000000000000003711570234561010056 0ustar usr/bin var/lib/ncbi-blast+/db debian/ncbi-blast+.manpages0000644000000000000000000000001311570234561012772 0ustar debian/*.1 debian/legacy/0000755000000000000000000000000012153003406010424 5ustar debian/legacy/legacy.sh0000755000000000000000000000010111570464731012235 0ustar #!/bin/sh # Execute legacy blast exec legacy_blast ${0##*/} $@ debian/ncbi-blast+.10000644000000000000000000000252311570234561011347 0ustar .TH ncbi-blast+ 1 "April 29, 2011" "version 2.2.25" "USER COMMANDS" .SH NAME ncbi-blast+ \- NCBI command tools for BLAST+ .SH ONELINE DOCUMENTATION .B BLAST+ documentation is available online at http://www.ncbi.nlm.nih.gov/books/NBK1763/ .PP .SH DESCRIPTION The NCBI BLAST+ is a group of tools for basic alignment search. BLAST+ is a rewrite of BLAST with new features and performance improvements. BLAST+ commands differ from original BLAST. For BLAST users, one should read the BLAST USERS paragraph. .PP .SH CONFIGURATION BLAST+ uses the BLASTDB environment variable to get default db directory. It is possible to update the file /etc/ncbi/.ncbirc to add the following: .B [BLAST] .B BLASTDB=/var/lib/ncbi-blast+/db .SH BLAST USERS The easiest way to get started using these command line applications is by means of the legacy_blast.pl PERL script which is bundled along with the BLAST+ applications. To utilize this script, simply prefix it to the invocation of the C toolkit BLAST command line application and append the --path option pointing to the installation directory of the BLAST+ applications. For example, instead of using .B blastall -i query -d nr -o blast.out use .B legacy_blast.pl blastall -i query -d nr -o blast.out --path /usr/bin .PP .SH AUTHOR Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging NCBI - BLAST+ debian/ncbi-blast+.dirs0000644000000000000000000000003411570464731012147 0ustar usr/bin usr/lib/ncbi-blast+ debian/patches/0000755000000000000000000000000012153003406010607 5ustar debian/patches/no_multiarch_rpath0000644000000000000000000000201312152773066014427 0ustar Subject: avoid redundant rpath entries on multiarch systems * src/build-system/configure(.ac): when ensuring that executables will be able to find libstdc++, don't add rpath entries that files under /etc/ld.so.conf.d already specify, even if they don't resemble traditional single-architecture or biarch locations. Debian-Bug: 633567. Author: Aaron M. Ucko Last-Update: 2011-08-28 --- a/c++/src/build-system/configure +++ b/c++/src/build-system/configure @@ -5923,7 +5923,7 @@ break ;; /* ) - found=true + fgrep -qsx $abs_dir /etc/ld.so.conf.d/* || found=true break ;; esac --- a/c++/src/build-system/configure.ac +++ b/c++/src/build-system/configure.ac @@ -1620,7 +1620,7 @@ break ;; /* ) - found=true + fgrep -qsx $abs_dir /etc/ld.so.conf.d/* || found=true break ;; esac debian/patches/wrong_path_to_touch.patch0000644000000000000000000003015511742121460015714 0ustar Subject: upstream bug using hard path for touch Description: upstream makes use of a hard path that does not match on hurd systems. Patch comes from upstream and will be included in next release Author: Olivier Sallou Last-Updated: 12/03/2012 --- a/c++/src/build-system/Makefile.meta.in +++ b/c++/src/build-system/Makefile.meta.in @@ -28,7 +28,7 @@ @make_shell@ RM = /bin/rm -TOUCH = /usr/bin/touch +TOUCH = @TOUCH@ MKDIR = /bin/mkdir signature = @signature@ --- a/c++/src/build-system/Makefile.mk.in +++ b/c++/src/build-system/Makefile.mk.in @@ -54,7 +54,7 @@ RMDIR = /bin/rm -rf COPY = /bin/cp -p BINCOPY = @BINCOPY@ -TOUCH = /usr/bin/touch +TOUCH = @TOUCH@ MKDIR = /bin/mkdir BINTOUCH = $(TOUCH) LN_S = @LN_S@ --- a/c++/src/build-system/NEWS +++ b/c++/src/build-system/NEWS @@ -8,3 +8,5 @@ 2011-05-17: new @ncbi_java@ variable for --with-jni builds. 2011-10-05: new @FEATURES@ variable for the unit test framework. + +2012-02-27: new @TOUCH@ variable to avoid hard-coded paths. --- a/c++/src/build-system/configure.ac +++ b/c++/src/build-system/configure.ac @@ -1965,6 +1965,7 @@ AC_MSG_RESULT(no) fi +AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH) AC_PROG_EGREP AC_MSG_CHECKING([how to run $EGREP quietly]) if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then --- a/c++/src/build-system/configure +++ b/c++/src/build-system/configure @@ -318,7 +318,7 @@ # include #endif" -ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS PROJECTS build build_cpu build_vendor build_os host host_cpu host_vendor host_os INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CC CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT CXX CXXFLAGS ac_ct_CXX MT_SFX DLL DLL_LIB_SETTING IF_WITH_DLL UNLESS_WITH_DLL STATIC USUAL_AND_DLL USUAL_AND_LIB LN_S RANLIB ac_ct_RANLIB AR STRIP DISTCC CCACHE TAIL EGREP VALGRIND_PATH CXXCPP TCHECK_CL AMQ CPP Z_INCLUDE Z_LIBS BZ2_INCLUDE BZ2_LIBS LZO_INCLUDE LZO_LIBS PCRE_INCLUDE PCRE_LIBS LIBGNUTLS_CONFIG GNUTLS_INCLUDE GNUTLS_LIBS OPENSSL_INCLUDE OPENSSL_LIBS FTDS64_INCLUDE FTDS64_LIBS FTDS64_LIB FTDS64_CTLIB_INCLUDE FTDS64_CTLIB_LIBS FTDS64_CTLIB_LIB FTDS_INCLUDE FTDS_LIBS FTDS_LIB freetds ftds64 mysql_config PYTHON PYTHON_INCLUDE PYTHON_LIBS PYTHON23 PYTHON23_INCLUDE PYTHON23_LIBS PYTHON24 PYTHON24_INCLUDE PYTHON24_LIBS PYTHON25 PYTHON25_INCLUDE PYTHON25_LIBS _ACJNI_JAVAC X_CFLAGS X_PRE_LIBS X_LIBS X_EXTRA_LIBS wxconf EXPAT_INCLUDE EXPAT_LIBS SABLOT_INCLUDE SABLOT_LIBS LIBXML_INCLUDE LIBXML_LIBS LIBXSLT_INCLUDE LIBXSLT_LIBS XSLTPROC SQLITE3_INCLUDE SQLITE3_LIBS OECHEM_INCLUDE OECHEM_LIBS SGE_INCLUDE SGE_LIBS MUPARSER_INCLUDE MUPARSER_LIBS HDF5_INCLUDE HDF5_LIBS JPEG_INCLUDE JPEG_LIBS PNG_INCLUDE PNG_LIBS TIFF_INCLUDE TIFF_LIBS UNGIF_INCLUDE UNGIF_LIBS GIF_INCLUDE GIF_LIBS XPM_INCLUDE XPM_LIBS freetype_config MAGIC_INCLUDE MAGIC_LIBS CURL_INCLUDE CURL_LIBS signature build_root top_srcdir srcdir status_dir builddir runpath ncbi_runpath c_ncbi_runpath LINK C_LINK TAIL_N EGREP_Q FAST_CFLAGS FAST_CXXFLAGS OBJCXX_CXXFLAGS DEPFLAGS DEPFLAGS_POST FAST_LDFLAGS APP_LDFLAGS DLL_LDFLAGS C_LIBS OBJCXX_LIBS GCCPCH RUNPATH_ORIGIN NO_STRICT_ALIASING D_SFX DEBUG_SFX LIB_OR_DLL FORCE_STATIC_LIB APP_LIB_SETTING APP_LIBS_SETTING LINK_DLL has_dll_loadable LINK_LOADABLE CFLAGS_DLL CXXFLAGS_DLL ALLOW_UNDEF FORBID_UNDEF OPT_GROUPS local_lbsm ncbi_crypt CONNEXT XCONNEXT serial bdb dbapi objects gui algo app internal sra check CHECK_ARG CHECK_TOOLS CHECK_TIMEOUT_MULT CHECK_OS_NAME FEATURES script_shell make_shell obj_ext lib_pre lib_l_pre lib_ext dll_ext loadable_ext lib_l_ext exe_ext f_compile f_outobj f_outlib f_libpath f_runpath f_outexe BDB_LIB BDB_CACHE_LIB DBAPI_DRIVER DBAPI_CTLIB DBAPI_DBLIB DBAPI_MYSQL DBAPI_ODBC THREAD_LIBS NCBIATOMIC_LIB NETWORK_LIBS NETWORK_PURE_LIBS RESOLVER_LIBS MATH_LIBS KSTAT_LIBS RPCSVC_LIBS CRYPT_LIBS DL_LIBS RT_LIBS UUID_LIBS DEMANGLE_LIBS ICONV_LIBS Z_LIB BZ2_LIB PCREPOSIX_LIBS PCRE_LIB OPENSSL_STATIC_LIBS TLS_INCLUDE TLS_LIBS SYBASE_PATH SYBASE_LCL_PATH SYBASE_INCLUDE SYBASE_LIBS SYBASE_DLLS SYBASE_DBLIBS MYSQL_INCLUDE MYSQL_LIBS BERKELEYDB_INCLUDE BERKELEYDB_LIBS BERKELEYDB_STATIC_LIBS BERKELEYDB_CXX_LIBS BERKELEYDB_CXX_STATIC_LIBS ODBC_INCLUDE ODBC_LIBS BOOST_INCLUDE BOOST_LIBPATH BOOST_TAG BOOST_REGEX_LIBS BOOST_REGEX_STATIC_LIBS BOOST_TEST_PEM_LIBS BOOST_TEST_PEM_STATIC_LIBS BOOST_TEST_TEM_LIBS BOOST_TEST_TEM_STATIC_LIBS BOOST_TEST_UTF_LIBS BOOST_TEST_UTF_STATIC_LIBS BOOST_THREAD_LIBS BOOST_THREAD_STATIC_LIBS NCBI_C_INCLUDE NCBI_C_LIBPATH OPENGL_INCLUDE OPENGL_LIBS OPENGL_STATIC_LIBS OSMESA_INCLUDE OSMESA_LIBS OSMESA_STATIC_LIBS GLUT_INCLUDE GLUT_LIBS GLEW_INCLUDE GLEW_LIBS GLEW_STATIC_LIBS FLTK_INCLUDE FLTK_LIBS FLTK_LIBS_GL FLTK_LIBS_IMAGES FLTK_LIBS_ALL FLTK_STATIC_LIBS FLTK_STATIC_LIBS_GL FLTK_STATIC_LIBS_IMAGES FLTK_STATIC_LIBS_ALL FLTK_CONFIG WXWIDGETS_INCLUDE WXWIDGETS_LIBS WXWIDGETS_STATIC_LIBS WXWIDGETS_GL_LIBS WXWIDGETS_GL_STATIC_LIBS WXWIDGETS_POST_LINK FASTCGI_INCLUDE FASTCGI_LIBS FASTCGI_OBJS NCBI_SSS_INCLUDE NCBI_SSS_LIBPATH LIBSSSUTILS LIBSSSDB sssutils SP_INCLUDE SP_LIBS ORBACUS_INCLUDE ORBACUS_LIBPATH LIBOB LIBIMR ICU_CONFIG ICU_INCLUDE ICU_LIBS ICU_STATIC_LIBS EXPAT_STATIC_LIBS SABLOT_STATIC_LIBS LIBXML_STATIC_LIBS LIBXSLT_STATIC_LIBS XERCES_INCLUDE XERCES_LIBS XERCES_STATIC_LIBS XALAN_INCLUDE XALAN_LIBS XALAN_STATIC_LIBS SQLITE3_STATIC_LIBS FREETYPE_INCLUDE FREETYPE_LIBS ncbi_xreader_pubseqos ncbi_xreader_pubseqos2 UNLESS_PUBSEQOS JDK_PATH JDK_INCLUDE ncbi_java NCBI_C_ncbi BINCOPY APP_NOCOPY APP_OR_NULL IF_REBUILDING_LIBS IF_REBUILDING_CONDITIONALLY IF_DEACTIVATING configurables_mfname CC_FILTER CXX_FILTER AR_FILTER LINK_FILTER CC_WRAPPER CXX_WRAPPER AR_WRAPPER LINK_WRAPPER KeepStateTarget Rules serial_ws50_rtti_kludge ncbicntr UNIX_SRC UNIX_USR_PROJ compiler compiler_root compiler_version COMPILER OSTYPE NCBI_PLATFORM_BITS LIBOBJS LTLIBOBJS' +ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS PROJECTS build build_cpu build_vendor build_os host host_cpu host_vendor host_os INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CC CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT CXX CXXFLAGS ac_ct_CXX MT_SFX DLL DLL_LIB_SETTING IF_WITH_DLL UNLESS_WITH_DLL STATIC USUAL_AND_DLL USUAL_AND_LIB LN_S RANLIB ac_ct_RANLIB AR STRIP DISTCC CCACHE TAIL TOUCH EGREP VALGRIND_PATH CXXCPP TCHECK_CL AMQ CPP Z_INCLUDE Z_LIBS BZ2_INCLUDE BZ2_LIBS LZO_INCLUDE LZO_LIBS PCRE_INCLUDE PCRE_LIBS LIBGNUTLS_CONFIG GNUTLS_INCLUDE GNUTLS_LIBS OPENSSL_INCLUDE OPENSSL_LIBS FTDS64_INCLUDE FTDS64_LIBS FTDS64_LIB FTDS64_CTLIB_INCLUDE FTDS64_CTLIB_LIBS FTDS64_CTLIB_LIB FTDS_INCLUDE FTDS_LIBS FTDS_LIB freetds ftds64 mysql_config PYTHON PYTHON_INCLUDE PYTHON_LIBS PYTHON23 PYTHON23_INCLUDE PYTHON23_LIBS PYTHON24 PYTHON24_INCLUDE PYTHON24_LIBS PYTHON25 PYTHON25_INCLUDE PYTHON25_LIBS _ACJNI_JAVAC X_CFLAGS X_PRE_LIBS X_LIBS X_EXTRA_LIBS wxconf EXPAT_INCLUDE EXPAT_LIBS SABLOT_INCLUDE SABLOT_LIBS LIBXML_INCLUDE LIBXML_LIBS LIBXSLT_INCLUDE LIBXSLT_LIBS XSLTPROC SQLITE3_INCLUDE SQLITE3_LIBS OECHEM_INCLUDE OECHEM_LIBS SGE_INCLUDE SGE_LIBS MUPARSER_INCLUDE MUPARSER_LIBS HDF5_INCLUDE HDF5_LIBS JPEG_INCLUDE JPEG_LIBS PNG_INCLUDE PNG_LIBS TIFF_INCLUDE TIFF_LIBS UNGIF_INCLUDE UNGIF_LIBS GIF_INCLUDE GIF_LIBS XPM_INCLUDE XPM_LIBS freetype_config MAGIC_INCLUDE MAGIC_LIBS CURL_INCLUDE CURL_LIBS signature build_root top_srcdir srcdir status_dir builddir runpath ncbi_runpath c_ncbi_runpath LINK C_LINK TAIL_N EGREP_Q FAST_CFLAGS FAST_CXXFLAGS OBJCXX_CXXFLAGS DEPFLAGS DEPFLAGS_POST FAST_LDFLAGS APP_LDFLAGS DLL_LDFLAGS C_LIBS OBJCXX_LIBS GCCPCH RUNPATH_ORIGIN NO_STRICT_ALIASING D_SFX DEBUG_SFX LIB_OR_DLL FORCE_STATIC_LIB APP_LIB_SETTING APP_LIBS_SETTING LINK_DLL has_dll_loadable LINK_LOADABLE CFLAGS_DLL CXXFLAGS_DLL ALLOW_UNDEF FORBID_UNDEF OPT_GROUPS local_lbsm ncbi_crypt CONNEXT XCONNEXT serial bdb dbapi objects gui algo app internal sra check CHECK_ARG CHECK_TOOLS CHECK_TIMEOUT_MULT CHECK_OS_NAME FEATURES script_shell make_shell obj_ext lib_pre lib_l_pre lib_ext dll_ext loadable_ext lib_l_ext exe_ext f_compile f_outobj f_outlib f_libpath f_runpath f_outexe BDB_LIB BDB_CACHE_LIB DBAPI_DRIVER DBAPI_CTLIB DBAPI_DBLIB DBAPI_MYSQL DBAPI_ODBC THREAD_LIBS NCBIATOMIC_LIB NETWORK_LIBS NETWORK_PURE_LIBS RESOLVER_LIBS MATH_LIBS KSTAT_LIBS RPCSVC_LIBS CRYPT_LIBS DL_LIBS RT_LIBS UUID_LIBS DEMANGLE_LIBS ICONV_LIBS Z_LIB BZ2_LIB PCREPOSIX_LIBS PCRE_LIB OPENSSL_STATIC_LIBS TLS_INCLUDE TLS_LIBS SYBASE_PATH SYBASE_LCL_PATH SYBASE_INCLUDE SYBASE_LIBS SYBASE_DLLS SYBASE_DBLIBS MYSQL_INCLUDE MYSQL_LIBS BERKELEYDB_INCLUDE BERKELEYDB_LIBS BERKELEYDB_STATIC_LIBS BERKELEYDB_CXX_LIBS BERKELEYDB_CXX_STATIC_LIBS ODBC_INCLUDE ODBC_LIBS BOOST_INCLUDE BOOST_LIBPATH BOOST_TAG BOOST_REGEX_LIBS BOOST_REGEX_STATIC_LIBS BOOST_TEST_PEM_LIBS BOOST_TEST_PEM_STATIC_LIBS BOOST_TEST_TEM_LIBS BOOST_TEST_TEM_STATIC_LIBS BOOST_TEST_UTF_LIBS BOOST_TEST_UTF_STATIC_LIBS BOOST_THREAD_LIBS BOOST_THREAD_STATIC_LIBS NCBI_C_INCLUDE NCBI_C_LIBPATH OPENGL_INCLUDE OPENGL_LIBS OPENGL_STATIC_LIBS OSMESA_INCLUDE OSMESA_LIBS OSMESA_STATIC_LIBS GLUT_INCLUDE GLUT_LIBS GLEW_INCLUDE GLEW_LIBS GLEW_STATIC_LIBS FLTK_INCLUDE FLTK_LIBS FLTK_LIBS_GL FLTK_LIBS_IMAGES FLTK_LIBS_ALL FLTK_STATIC_LIBS FLTK_STATIC_LIBS_GL FLTK_STATIC_LIBS_IMAGES FLTK_STATIC_LIBS_ALL FLTK_CONFIG WXWIDGETS_INCLUDE WXWIDGETS_LIBS WXWIDGETS_STATIC_LIBS WXWIDGETS_GL_LIBS WXWIDGETS_GL_STATIC_LIBS WXWIDGETS_POST_LINK FASTCGI_INCLUDE FASTCGI_LIBS FASTCGI_OBJS NCBI_SSS_INCLUDE NCBI_SSS_LIBPATH LIBSSSUTILS LIBSSSDB sssutils SP_INCLUDE SP_LIBS ORBACUS_INCLUDE ORBACUS_LIBPATH LIBOB LIBIMR ICU_CONFIG ICU_INCLUDE ICU_LIBS ICU_STATIC_LIBS EXPAT_STATIC_LIBS SABLOT_STATIC_LIBS LIBXML_STATIC_LIBS LIBXSLT_STATIC_LIBS XERCES_INCLUDE XERCES_LIBS XERCES_STATIC_LIBS XALAN_INCLUDE XALAN_LIBS XALAN_STATIC_LIBS SQLITE3_STATIC_LIBS FREETYPE_INCLUDE FREETYPE_LIBS ncbi_xreader_pubseqos ncbi_xreader_pubseqos2 UNLESS_PUBSEQOS JDK_PATH JDK_INCLUDE ncbi_java NCBI_C_ncbi BINCOPY APP_NOCOPY APP_OR_NULL IF_REBUILDING_LIBS IF_REBUILDING_CONDITIONALLY IF_DEACTIVATING configurables_mfname CC_FILTER CXX_FILTER AR_FILTER LINK_FILTER CC_WRAPPER CXX_WRAPPER AR_WRAPPER LINK_WRAPPER KeepStateTarget Rules serial_ws50_rtti_kludge ncbicntr UNIX_SRC UNIX_USR_PROJ compiler compiler_root compiler_version COMPILER OSTYPE NCBI_PLATFORM_BITS LIBOBJS LTLIBOBJS' ac_subst_files='' # Initialize some variables set by options. @@ -6615,6 +6615,46 @@ echo "${ECHO_T}no" >&6 fi +# Extract the first word of "touch", so it can be a program name with args. +set dummy touch; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_path_TOUCH+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + case $TOUCH in + [\\/]* | ?:[\\/]*) + ac_cv_path_TOUCH="$TOUCH" # Let the user override the test with a path. + ;; + *) + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +as_dummy="/bin:/usr/bin:$PATH" +for as_dir in $as_dummy +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_path_TOUCH="$as_dir/$ac_word$ac_exec_ext" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + + ;; +esac +fi +TOUCH=$ac_cv_path_TOUCH + +if test -n "$TOUCH"; then + echo "$as_me:$LINENO: result: $TOUCH" >&5 +echo "${ECHO_T}$TOUCH" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + echo "$as_me:$LINENO: checking for egrep" >&5 echo $ECHO_N "checking for egrep... $ECHO_C" >&6 if test "${ac_cv_prog_egrep+set}" = set; then @@ -33848,6 +33888,7 @@ s,@DISTCC@,$DISTCC,;t t s,@CCACHE@,$CCACHE,;t t s,@TAIL@,$TAIL,;t t +s,@TOUCH@,$TOUCH,;t t s,@EGREP@,$EGREP,;t t s,@VALGRIND_PATH@,$VALGRIND_PATH,;t t s,@CXXCPP@,$CXXCPP,;t t debian/patches/fix_arm_mips_build0000644000000000000000000000124612033555552014404 0ustar Subject: FTBS issue on ARM and MIPS Descrition: switch NCBI_BIG_TYPE's baseline to Int8 from NCBI_INT8_TYPE to fix build failures on Linux systems with ARM or MIPS processors, which have inttypes.h and lack an extra-wide scalar type. Bug fixed upstream. Last-Updated: 2012-09-25 Author: Aaron Ucko Forwarded: not-needed --- trunk/c++/include/corelib/ncbitype.h 2012/06/01 19:13:24 54673 +++ trunk/c++/include/corelib/ncbitype.h 2012/09/24 14:15:47 55773 @@ -150,7 +150,7 @@ /* BigScalar */ -#define NCBI_BIG_TYPE NCBI_INT8_TYPE +#define NCBI_BIG_TYPE Int8 #define SIZEOF_NCBI_BIG 8 #if (SIZEOF_LONG_DOUBLE > SIZEOF_NCBI_BIG) # undef NCBI_BIG_TYPE debian/patches/legacy_rename_rpsblast0000644000000000000000000000067511742121460015253 0ustar Author: Olivier Sallou Description: rename binary as blast+ for package coherency. Last-Updated: 2011-10-03 --- a/c++/src/app/blast/legacy_blast.pl +++ b/c++/src/app/blast/legacy_blast.pl @@ -1064,7 +1064,7 @@ if (defined $opt_p and $opt_p =~ /f/i) { $retval .= "/rpstblastn"; } else { - $retval .= "/rpsblast"; + $retval .= "/rpsblast+"; } $retval .= &add_exe_extension(); debian/patches/fix_checks0000644000000000000000000000124411742121460012645 0ustar Subject: checks misreported as absent when unpacked under /*/src/* * src/build-system/Makefile.meta.in: supply it to check_add.sh Author: Aaron M. Ucko Last-Update: 2011-05-23 --- a/c++/src/build-system/Makefile.meta.in 2011-05-23 18:48:59.000000000 -0400 +++ b/c++/src/build-system/Makefile.meta.in 2011-05-23 18:49:20.000000000 -0400 @@ -188,7 +188,7 @@ expendable=false ; \ for i in $$x_project ; do \ if test "x$$i" = "x-" ; then expendable=true ; continue ; fi ; \ - $(check_add) $(abs_srcdir) $$i @signature@ @exe_ext@ + $(check_add) $(abs_srcdir) $$i @signature@ $(subdir) CHECK_ADD_KET = || exit 5 ; \ done ; \ fi debian/patches/fix_lib_deps0000644000000000000000000004214612152773066013207 0ustar Subject: ensure that all libraries link against all direct dependencies * src/**/Makefile.*.lib: set DLL_(D)LIB correctly. 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. * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect rather than libconnect for consistency with libblast, which uses the former to keep the aforementioned cycle-breaking from causing inconsistency elsewhere. Debian-Bug: 633567. Author: Aaron M. Ucko Last-Update: 2011-08-28 --- a/c++/src/algo/blast/core/Makefile.blast.lib +++ b/c++/src/algo/blast/core/Makefile.blast.lib @@ -21,5 +21,6 @@ CFLAGS = $(FAST_CFLAGS) LDFLAGS = $(FAST_LDFLAGS) +DLL_LIB = composition_adjustment xconnect tables WATCHERS = coulouri maning madden camacho --- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib +++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib @@ -11,6 +11,8 @@ CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) +DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi + ASN_DEP = seqset WATCHERS = morgulis --- a/c++/src/algo/blast/format/Makefile.xblastformat.lib +++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib @@ -7,6 +7,7 @@ CPPFLAGS = $(ORIG_CPPFLAGS) -DLL_LIB = align_format blastxml xhtml xcgi +DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \ + seq general xser tables xncbi WATCHERS = jianye zaretska madden camacho fongah2 --- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib +++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib @@ -21,3 +21,4 @@ CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) +DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi --- a/c++/src/cgi/Makefile.cgi.lib +++ b/c++/src/cgi/Makefile.cgi.lib @@ -9,6 +9,8 @@ user_agent LIB = xcgi +DLL_LIB = xutil xncbi + CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) WATCHERS = vakatov --- a/c++/src/html/Makefile.html.lib +++ b/c++/src/html/Makefile.html.lib @@ -7,4 +7,6 @@ jsmenu commentdiag indentstream html_exception writer_htmlenc LIB = xhtml +DLL_LIB = xncbi + WATCHERS = ivanov --- a/c++/src/objects/blast/Makefile.xnetblastcli.lib +++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib @@ -2,3 +2,5 @@ LIB = xnetblastcli SRC = blastclient blastclient_ + +DLL_LIB = xnetblast xser xconnect xutil xncbi --- a/c++/src/objtools/align_format/Makefile.align_format.lib +++ b/c++/src/objtools/align_format/Makefile.align_format.lib @@ -13,6 +13,10 @@ CPPFLAGS = $(ORIG_CPPFLAGS) +DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \ + xobjmgr xnetblast blastdb gene_info seqset seq general xser \ + xcgi xhtml tables xncbi + ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST # CFLAGS = $(FAST_CFLAGS) # CXXFLAGS = $(FAST_CXXFLAGS) --- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib +++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib @@ -12,3 +12,5 @@ WATCHERS = todorov dicuccio grichenk +DLL_LIB = xobjmgr seqset seq xser tables xncbi + --- a/c++/src/objtools/readers/Makefile.xobjread.lib +++ b/c++/src/objtools/readers/Makefile.xobjread.lib @@ -19,5 +19,5 @@ best_feat_finder source_mod_parser fasta_exception -DLL_LIB = creaders +DLL_LIB = seqset seq pub general xser creaders sequtil xutil xncbi --- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib +++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib @@ -12,6 +12,6 @@ mask_writer_blastdb_maskinfo ASN_DEP = seqset -DLL_LIB = seqdb blastdb +DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi WATCHERS = morgulis camacho --- a/c++/src/objtools/simple/Makefile.xobjsimple.lib +++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib @@ -7,6 +7,8 @@ ASN_DEP = seqset +DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi + LIB = xobjsimple SRC = simple_om --- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib +++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib @@ -24,6 +24,8 @@ LIB = seqdb +DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi + CFLAGS = $(FAST_CFLAGS) CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) --- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib +++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib @@ -5,4 +5,6 @@ ASN_DEP = blastdb seqset +DLL_LIB = seqdb xobjmgr seqset seq xncbi + WATCHERS = camacho --- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib +++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib @@ -3,6 +3,8 @@ LIB = ncbi_xloader_blastdb_rmt SRC = bdbloader_rmt remote_blastdb_adapter +DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi + ASN_DEP = blastdb xnetblast WATCHERS = camacho --- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib +++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib @@ -4,3 +4,5 @@ LIB = gene_info SRC = gene_info gene_info_reader file_utils + +DLL_LIB = xncbi --- a/c++/src/algo/blast/api/Makefile.xblast.lib +++ b/c++/src/algo/blast/api/Makefile.xblast.lib @@ -74,14 +74,15 @@ deltablast_options \ deltablast -SRC = $(SRC_C:%=.core_%) $(SRC_CXX) +SRC = $(SRC_CXX) # $(SRC_C:%=.core_%) LIB = xblast DLL_LIB = xalgoblastdbindex composition_adjustment xalgowinmask \ xalgodustmask seqmasks_io seqdb $(OBJREAD_LIBS) xobjutil \ blastdb xnetblastcli xnetblast scoremat xconnect tables \ - $(SOBJMGR_LIBS) + $(SOBJMGR_LIBS) blast seqdb seqset seq general \ + xser xconnect sequtil tables xutil xncbi CFLAGS = $(FAST_CFLAGS) # Strict gcc flags --- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib +++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib @@ -24,7 +24,9 @@ LIB = blastinput -DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread $(OBJMGR_LIBS) xutil + DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \ + $(OBJMGR_LIBS) xutil ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \ + scoremat seqset seq xser xutil xncbi # should be redundant, given the above :-/ ASN_DEP = seqset xnetblast --- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib +++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib @@ -8,6 +8,8 @@ SRC = symdust +DLL_LIB = xobjmgr seq xncbi + CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) --- a/c++/src/connect/Makefile.xconnect.lib +++ b/c++/src/connect/Makefile.xconnect.lib @@ -14,6 +14,8 @@ LIB = xconnect PROJ_TAG = core +DLL_LIB = xncbi + LIBS = $(NETWORK_LIBS) $(ORIG_LIBS) WATCHERS = lavr --- a/c++/src/connect/ext/Makefile.xconnext.lib +++ b/c++/src/connect/ext/Makefile.xconnext.lib @@ -6,4 +6,6 @@ LIB = xconnext +DLL_LIB = xconnect xncbi + WATCHERS = lavr --- a/c++/src/objects/blast/Makefile.blast.lib +++ b/c++/src/objects/blast/Makefile.blast.lib @@ -1,4 +1,6 @@ LIB = xnetblast SRC = blast__ blast___ names +DLL_LIB = scoremat seqset seq xser xncbi + WATCHERS = camacho --- a/c++/src/objects/blastxml/Makefile.blastxml.lib +++ b/c++/src/objects/blastxml/Makefile.blastxml.lib @@ -1,2 +1,4 @@ LIB = blastxml SRC = blastxml__ blastxml___ + +DLL_LIB = xser xncbi --- a/c++/src/objects/entrez2/Makefile.entrez2.lib +++ b/c++/src/objects/entrez2/Makefile.entrez2.lib @@ -2,3 +2,5 @@ LIB = entrez2 SRC = entrez2__ entrez2___ + +DLL_LIB = xser xncbi --- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib +++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib @@ -4,3 +4,5 @@ LIB = entrez2cli SRC = entrez2_client entrez2_client_ + +DLL_LIB = entrez2 xser xconnect xutil xncbi --- a/c++/src/objects/scoremat/Makefile.scoremat.lib +++ b/c++/src/objects/scoremat/Makefile.scoremat.lib @@ -1,2 +1,4 @@ LIB = scoremat SRC = scoremat__ scoremat___ + +DLL_LIB = seqset seq general xser xncbi --- a/c++/src/objects/seqedit/Makefile.seqedit.lib +++ b/c++/src/objects/seqedit/Makefile.seqedit.lib @@ -1,3 +1,4 @@ LIB = seqedit SRC = seqedit__ seqedit___ - + +DLL_LIB = seqset seq general xser xncbi --- a/c++/src/objects/submit/Makefile.submit.lib +++ b/c++/src/objects/submit/Makefile.submit.lib @@ -1,2 +1,4 @@ LIB = submit SRC = submit__ submit___ + +DLL_LIB = seqset seq biblio general xser xncbi --- a/c++/src/objmgr/util/Makefile.util.lib +++ b/c++/src/objmgr/util/Makefile.util.lib @@ -8,5 +8,7 @@ SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util LIB = xobjutil +DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi + WATCHERS = ucko vasilche --- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib +++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib @@ -11,6 +11,7 @@ CPPFLAGS = $(ORIG_CPPFLAGS) +DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST # CFLAGS = $(FAST_CFLAGS) --- a/c++/src/objtools/blast/services/Makefile.blast_services.lib +++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib @@ -8,6 +8,8 @@ LIB = blast_services +DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi + CFLAGS = $(FAST_CFLAGS) CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) --- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib +++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib @@ -12,4 +12,7 @@ # Dependencies for shared library DLL_LIB = ncbi_xreader$(DLL) +DLL_DLIB = ncbi_xreader_id2 ncbi_xreader_id1 ncbi_xreader_cache ncbi_xreader \ + xobjmgr seq xutil xncbi + WATCHERS = vasilche --- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib +++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib @@ -15,4 +15,7 @@ DLL_LIB = DLL_DLIB = $(GENBANK_READER_LDEP) +DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \ + xser xconnect xcompress xutil xncbi + WATCHERS = vasilche --- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib +++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib @@ -12,6 +12,8 @@ # Dependencies for shared library DLL_LIB = ncbi_xreader$(DLL) +DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi + CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) WATCHERS = vasilche --- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib +++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib @@ -12,6 +12,8 @@ # Dependencies for shared library DLL_LIB = xconnect ncbi_xreader$(DLL) +DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi + CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) WATCHERS = vasilche --- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib +++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib @@ -12,6 +12,9 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE) # Dependencies for shared library (disabled due to problems on Darwin) -# DLL_LIB = xconnect ncbi_xreader$(DLL) +DLL_LIB = xconnect ncbi_xreader$(DLL) + +DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi + WATCHERS = vasilche --- a/c++/src/util/compress/api/Makefile.compress.lib +++ b/c++/src/util/compress/api/Makefile.compress.lib @@ -6,7 +6,7 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) -DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) +DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) WATCHERS = ivanov --- a/c++/src/util/sequtil/Makefile.sequtil.lib +++ b/c++/src/util/sequtil/Makefile.sequtil.lib @@ -3,4 +3,6 @@ LIB = sequtil SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared +DLL_LIB = xncbi + WATCHERS = shomrat --- a/c++/src/corelib/Makefile.test_boost.lib +++ b/c++/src/corelib/Makefile.test_boost.lib @@ -3,6 +3,8 @@ SRC = test_boost LIB = test_boost +DLL_LIB = xncbi + CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) REQUIRES = Boost.Test.Included --- a/c++/src/corelib/Makefile.test_mt.lib +++ b/c++/src/corelib/Makefile.test_mt.lib @@ -3,6 +3,8 @@ SRC = test_mt LIB = test_mt +DLL_LIB = xncbi + # REQUIRES = MT USE_PCH = no --- a/c++/src/objects/biblio/Makefile.biblio.lib +++ b/c++/src/objects/biblio/Makefile.biblio.lib @@ -1,2 +1,4 @@ LIB = biblio SRC = biblio__ biblio___ citation_base + +DLL_LIB = general xser xncbi --- a/c++/src/objects/blastdb/Makefile.blastdb.lib +++ b/c++/src/objects/blastdb/Makefile.blastdb.lib @@ -1,2 +1,4 @@ LIB = blastdb SRC = blastdb__ blastdb___ + +DLL_LIB = seq xser xncbi --- a/c++/src/objects/general/Makefile.general.lib +++ b/c++/src/objects/general/Makefile.general.lib @@ -1,2 +1,4 @@ LIB = general SRC = general__ general___ uoconv + +DLL_LIB = xser xncbi --- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib +++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib @@ -3,4 +3,6 @@ LIB = genome_collection SRC = genome_collection__ genome_collection___ +DLL_LIB = seq general xser xncbi + WATCHERS = dicuccio --- a/c++/src/objects/id1/Makefile.id1.lib +++ b/c++/src/objects/id1/Makefile.id1.lib @@ -3,4 +3,6 @@ LIB = id1 SRC = id1__ id1___ +DLL_LIB = seqset seq xser xncbi + WATCHERS = vasilche --- a/c++/src/objects/id2/Makefile.id2.lib +++ b/c++/src/objects/id2/Makefile.id2.lib @@ -1,4 +1,6 @@ LIB = id2 SRC = id2__ id2___ +DLL_LIB = seqsplit seq xser xncbi + WATCHERS = vasilche --- a/c++/src/objects/medline/Makefile.medline.lib +++ b/c++/src/objects/medline/Makefile.medline.lib @@ -1,2 +1,4 @@ LIB = medline SRC = medline__ medline___ + +DLL_LIB = biblio general xser xncbi --- a/c++/src/objects/pub/Makefile.pub.lib +++ b/c++/src/objects/pub/Makefile.pub.lib @@ -1,2 +1,4 @@ LIB = pub SRC = pub__ pub___ + +DLL_LIB = medline biblio xser xncbi --- a/c++/src/objects/seq/Makefile.seq.lib +++ b/c++/src/objects/seq/Makefile.seq.lib @@ -12,4 +12,6 @@ seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \ seq_loc_from_string seq_loc_reverse_complementer +DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi + WATCHERS = vasilche grichenk --- a/c++/src/objects/seqcode/Makefile.seqcode.lib +++ b/c++/src/objects/seqcode/Makefile.seqcode.lib @@ -1,2 +1,4 @@ LIB = seqcode SRC = seqcode__ seqcode___ + +DLL_LIB = xser xncbi --- a/c++/src/objects/seqset/Makefile.seqset.lib +++ b/c++/src/objects/seqset/Makefile.seqset.lib @@ -1,2 +1,4 @@ LIB = seqset SRC = seqset__ seqset___ gb_release_file + +DLL_LIB = seq general xser xncbi --- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib +++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib @@ -1,4 +1,6 @@ LIB = seqsplit SRC = seqsplit__ seqsplit___ +DLL_LIB = seqset seq xser xncbi + WATCHERS = vasilche --- a/c++/src/serial/Makefile.serial.lib +++ b/c++/src/serial/Makefile.serial.lib @@ -18,4 +18,6 @@ LIB = xser +DLL_LIB = xutil xncbi + WATCHERS = gouriano --- a/c++/src/util/Makefile.util.lib +++ b/c++/src/util/Makefile.util.lib @@ -11,6 +11,7 @@ LIB = xutil PROJ_TAG = core +DLL_LIB = xncbi LIBS = $(ORIG_LIBS) WATCHERS = vakatov --- a/c++/src/util/xregexp/Makefile.xregexp.lib +++ b/c++/src/util/xregexp/Makefile.xregexp.lib @@ -6,7 +6,7 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE) -DLL_LIB = $(PCRE_LIB) +DLL_LIB = $(PCRE_LIB) xncbi LIBS = $(PCRE_LIBS) WATCHERS = ivanov --- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib +++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib @@ -8,6 +8,8 @@ SRC = segmask +DLL_LIB = blast xobjmgr xncbi + CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) --- a/c++/src/objmgr/split/Makefile.id2_split.lib +++ b/c++/src/objmgr/split/Makefile.id2_split.lib @@ -17,6 +17,6 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) -DLL_LIB = $(SOBJMGR_LIBS) +DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi WATCHERS = vasilche --- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib +++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib @@ -8,6 +8,9 @@ LIB = writedb +DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \ + xser sequtil xutil xncbi + CFLAGS = $(FAST_CFLAGS) CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) --- a/c++/src/algo/blast/Makefile.blast_macros.mk +++ b/c++/src/algo/blast/Makefile.blast_macros.mk @@ -18,7 +18,7 @@ BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS) # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS -BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \ +BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \ xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \ xobjread creaders xnetblastcli xnetblast blastdb scoremat tables xalnmgr # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS) --- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app +++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app @@ -2,7 +2,7 @@ SRC = main mkindex_app LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \ - xobjread creaders xobjutil tables connect $(SOBJMGR_LIBS) + xobjread creaders xobjutil tables xconnect $(SOBJMGR_LIBS) LIB = $(LIB_:%=%$(STATIC)) CXXFLAGS = $(FAST_CXXFLAGS) debian/patches/support_other_cpus0000644000000000000000000000644411625022025014512 0ustar Subject: build correctly on architectures that wound up w/NCBI_SLOW_ATOMIC_SWAP * include/corelib/impl/ncbi_atomic_defs.h, include/corelib/ncbiatomic.h: fix powerpc detection, which previously only worked under Darwin. * src/objects/seq/seq_id_*.hpp: move sx_GetSeqIdMutex to join its users. Author: Aaron M. Ucko Last-Update: 2011-06-08 Index: b/c++/include/corelib/impl/ncbi_atomic_defs.h =================================================================== --- a/c++/include/corelib/impl/ncbi_atomic_defs.h 2011-06-08 20:26:07.000000000 -0400 +++ b/c++/include/corelib/impl/ncbi_atomic_defs.h 2011-06-08 20:29:25.000000000 -0400 @@ -259,7 +259,7 @@ # endif #endif -#if !defined(NCBI_SWAP_POINTERS) && !defined(NCBI_SWAP_POINTERS_CONDITIONALLY) && !defined(NCBI_NO_THREADS) && (!defined(NCBI_COUNTER_ASM_OK) || (!defined(__i386) && !defined(__ppc__) && !defined(__ppc64__) && !defined(__sparc) && !defined(__x86_64))) +#if !defined(NCBI_SWAP_POINTERS) && !defined(NCBI_SWAP_POINTERS_CONDITIONALLY) && !defined(NCBI_NO_THREADS) && (!defined(NCBI_COUNTER_ASM_OK) || (!defined(__i386) && !defined(__powerpc__) && !defined(__powerpc64__) && !defined(__ppc__) && !defined(__ppc64__) && !defined(__sparc) && !defined(__x86_64))) # define NCBI_SWAP_POINTERS_EXTERN 1 # define NCBI_SLOW_ATOMIC_SWAP 1 #endif Index: b/c++/include/corelib/ncbiatomic.h =================================================================== --- a/c++/include/corelib/ncbiatomic.h 2011-06-08 20:26:00.000000000 -0400 +++ b/c++/include/corelib/ncbiatomic.h 2011-06-08 20:30:34.000000000 -0400 @@ -121,14 +121,14 @@ asm volatile("swap [%2], %1" : "=m" (*nv_loc), "=r" (old_value) : "r" (nv_loc), "1" (new_value), "m" (*nv_loc)); return old_value; -# elif defined(__ppc__) || defined(__ppc64__) +# elif defined(__powerpc__) || defined(__powerpc64__) || defined(__ppc__) || defined(__ppc64__) void* old_value; int swapped = 0; NCBI_SCHED_SPIN_INIT(); while ( !swapped ) { swapped = 0; asm volatile( -#ifdef __ppc64__ +#if defined(__powerpc64__) || defined(__ppc64__) "ldarx %1,0,%4\n\tstdcx. %3,0,%4" #else "lwarx %1,0,%4\n\tstwcx. %3,0,%4" Index: b/c++/src/objects/seq/seq_id_handle.cpp =================================================================== --- a/c++/src/objects/seq/seq_id_handle.cpp 2011-06-08 20:26:34.000000000 -0400 +++ b/c++/src/objects/seq/seq_id_handle.cpp 2011-06-08 20:28:43.000000000 -0400 @@ -47,11 +47,6 @@ // CSeq_id_Info // -//#define NCBI_SLOW_ATOMIC_SWAP -#ifdef NCBI_SLOW_ATOMIC_SWAP -DEFINE_STATIC_FAST_MUTEX(sx_GetSeqIdMutex); -#endif - CSeq_id_Info::CSeq_id_Info(CSeq_id::E_Choice type, CSeq_id_Mapper* mapper) Index: b/c++/src/objects/seq/seq_id_tree.cpp =================================================================== --- a/c++/src/objects/seq/seq_id_tree.cpp 2011-06-08 20:26:34.000000000 -0400 +++ b/c++/src/objects/seq/seq_id_tree.cpp 2011-06-08 20:28:53.000000000 -0400 @@ -42,6 +42,11 @@ BEGIN_NCBI_SCOPE BEGIN_SCOPE(objects) +//#define NCBI_SLOW_ATOMIC_SWAP +#ifdef NCBI_SLOW_ATOMIC_SWAP +DEFINE_STATIC_FAST_MUTEX(sx_GetSeqIdMutex); +#endif + //////////////////////////////////////////////////////////////////// // // CSeq_id_***_Tree:: debian/patches/fix_gcc47_errors0000644000000000000000000002570111753041455013723 0ustar Subject: fix various GCC 4.7 compilation errors and warnings * 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. Author: Aaron M. Ucko Last-Update: 2012-04-13 --- a/c++/include/connect/ncbi_conn_stream.hpp +++ b/c++/include/connect/ncbi_conn_stream.hpp @@ -259,7 +259,7 @@ class CConn_IOStreamSetReadTimeout : protected CConn_IOStreamSetTimeout { public: - CConn_IOStreamSetTimeout::GetTimeout; + using CConn_IOStreamSetTimeout::GetTimeout; protected: CConn_IOStreamSetReadTimeout(const STimeout* timeout) @@ -289,7 +289,7 @@ class CConn_IOStreamSetWriteTimeout : protected CConn_IOStreamSetTimeout { public: - CConn_IOStreamSetTimeout::GetTimeout; + using CConn_IOStreamSetTimeout::GetTimeout; protected: CConn_IOStreamSetWriteTimeout(const STimeout* timeout) --- a/c++/include/corelib/ncbiexpt.hpp +++ b/c++/include/corelib/ncbiexpt.hpp @@ -852,7 +852,7 @@ exception_class(const exception_class& other) \ : base_class(other) \ { \ - x_Assign(other); \ + this->x_Assign(other); \ } \ public: \ virtual ~exception_class(void) throw() {} \ @@ -1172,7 +1172,7 @@ : TBase( other) { m_Errno = other.m_Errno; - x_Assign(other); + this->x_Assign(other); } /// Destructor. --- a/c++/include/corelib/ncbimisc.hpp +++ b/c++/include/corelib/ncbimisc.hpp @@ -39,6 +39,7 @@ #ifdef HAVE_SYS_TYPES_H # include #endif +#include #ifdef NCBI_COMPILER_ICC // Preemptively pull in , which breaks if we've already // repointed is* at NCBI_is*. --- a/c++/include/corelib/ncbistl.hpp +++ b/c++/include/corelib/ncbistl.hpp @@ -37,6 +37,7 @@ #include +#include // Get rid of some warnings in MSVC++ #if (_MSC_VER >= 1200) --- a/c++/include/corelib/ncbistr.hpp +++ b/c++/include/corelib/ncbistr.hpp @@ -3039,7 +3039,7 @@ : TBase(other) { m_Pos = other.m_Pos; - x_Assign(other); + this->x_Assign(other); } /// Destructor. --- a/c++/include/serial/impl/stltypes.hpp +++ b/c++/include/serial/impl/stltypes.hpp @@ -412,6 +412,7 @@ typedef StlIterator TStlIterator; typedef TypeInfoIterator TTypeInfoIterator; typedef typename TTypeInfoIterator::TObjectPtr TObjectPtr; + typedef CStlClassInfoFunctions CParent; static TStlIterator& It(TTypeInfoIterator& iter) { @@ -437,7 +438,8 @@ } static bool InitIterator(TTypeInfoIterator& iter) { - TStlIterator stl_iter = Get(iter.GetContainerPtr()).begin(); + TStlIterator stl_iter + = CParent::Get(iter.GetContainerPtr()).begin(); if ( sizeof(TStlIterator) <= sizeof(iter.m_IteratorData) ) { void* data = &iter.m_IteratorData; new (data) TStlIterator(stl_iter); @@ -445,7 +447,7 @@ else { iter.m_IteratorData = new TStlIterator(stl_iter); } - return stl_iter != Get(iter.GetContainerPtr()).end(); + return stl_iter != CParent::Get(iter.GetContainerPtr()).end(); } static void ReleaseIterator(TTypeInfoIterator& iter) { @@ -466,7 +468,7 @@ static bool NextElement(TTypeInfoIterator& iter) { - return ++It(iter) != Get(iter.GetContainerPtr()).end(); + return ++It(iter) != CParent::Get(iter.GetContainerPtr()).end(); } static TObjectPtr GetElementPtr(const TTypeInfoIterator& iter) { @@ -503,7 +505,7 @@ static bool EraseElement(TTypeInfoIterator& iter) { - TStlIterator& it = It(iter); + TStlIterator& it = CParent::It(iter); Container* c = static_cast(iter.GetContainerPtr()); it = c->erase(it); return it != c->end(); @@ -511,7 +513,7 @@ static void EraseAllElements(TTypeInfoIterator& iter) { Container* c = static_cast(iter.GetContainerPtr()); - c->erase(It(iter), c->end()); + c->erase(CParent::It(iter), c->end()); } static void SetIteratorFunctions(CStlOneArgTemplate* info) @@ -542,7 +544,7 @@ } static bool EraseElement(TTypeInfoIterator& iter) { - TStlIterator& it = It(iter); + TStlIterator& it = CParent::It(iter); Container* c = static_cast(iter.GetContainerPtr()); TStlIterator erase = it++; c->erase(erase); @@ -551,7 +553,7 @@ static void EraseAllElements(TTypeInfoIterator& iter) { Container* c = static_cast(iter.GetContainerPtr()); - c->erase(It(iter), c->end()); + c->erase(CParent::It(iter), c->end()); } static void SetIteratorFunctions(CStlOneArgTemplate* info) --- a/c++/include/serial/iterator.hpp +++ b/c++/include/serial/iterator.hpp @@ -520,13 +520,13 @@ CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo) : m_NeedType(needType) { - Init(beginInfo); + this->Init(beginInfo); } CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo, const string& filter) : m_NeedType(needType) { - Init(beginInfo, filter); + this->Init(beginInfo, filter); } virtual bool CanSelect(const CConstObjectInfo& object) --- a/c++/include/util/bitset/bmfunc.h +++ b/c++/include/util/bitset/bmfunc.h @@ -39,6 +39,13 @@ namespace bm { +bm::id_t bit_block_any_range(const bm::word_t* block, + bm::word_t left, + bm::word_t right); + +bm::id_t bit_block_calc_count_range(const bm::word_t* block, + bm::word_t left, + bm::word_t right); /*! @brief Structure with statistical information about bitset's memory --- a/c++/include/util/bitset/bmserial.h +++ b/c++/include/util/bitset/bmserial.h @@ -1381,7 +1381,7 @@ case set_block_arrgap: case set_block_arrgap_egamma: { - unsigned arr_len = read_id_list(dec, btype, this->id_array_); + unsigned arr_len = this->read_id_list(dec, btype, this->id_array_); gap_len = gap_set_array(gap_temp_block_, this->id_array_, arr_len); break; } @@ -1390,7 +1390,7 @@ (sizeof(gap_word_t) == 2 ? dec.get_16() : dec.get_32()); case set_block_arrgap_egamma_inv: case set_block_arrgap_inv: - gap_len = read_gap_block(dec, btype, gap_temp_block_, gap_head); + gap_len = this->read_gap_block(dec, btype, gap_temp_block_, gap_head); break; default: BM_ASSERT(0); --- a/c++/include/util/linkedset.hpp +++ b/c++/include/util/linkedset.hpp @@ -268,10 +268,10 @@ pair ins = m_Container.insert(value); if ( ins.second ) { if ( ins.first == begin() ) - insertToStart(*ins.first); + this->insertToStart(*ins.first); else { iterator prev = ins.first; - insertAfter(*--prev, *ins.first); + this->insertAfter(*--prev, *ins.first); } } return ins; @@ -280,10 +280,10 @@ void erase(iterator iter) { if ( iter == begin() ) - removeFromStart(*iter); + this->removeFromStart(*iter); else { iterator prev = iter; - removeAfter(*--prev, *iter); + this->removeAfter(*--prev, *iter); } m_Container.erase(iter); } @@ -422,10 +422,10 @@ { iterator iter = m_Container.insert(value); if ( iter == begin() ) - insertToStart(get(iter)); + this->insertToStart(get(iter)); else { iterator prev = iter; - insertAfter(get(--prev), get(iter)); + this->insertAfter(get(--prev), get(iter)); } return iter; } @@ -433,10 +433,10 @@ void erase(iterator iter) { if ( iter == begin() ) - removeFromStart(get(iter)); + this->removeFromStart(get(iter)); else { iterator prev = iter; - removeAfter(get(--prev), get(iter)); + this->removeAfter(get(--prev), get(iter)); } m_Container.erase(iter); } --- a/c++/include/util/rangemap.hpp +++ b/c++/include/util/rangemap.hpp @@ -578,7 +578,7 @@ // get level // insert element - TSelectMapI selectIter = insertLevel(selectKey); + TSelectMapI selectIter = this->insertLevel(selectKey); pair levelIns = selectIter->second.insert(value); pair ret; @@ -640,7 +640,7 @@ // insert element iterator ret; ret.m_Range = range_type::GetWhole(); - ret.m_SelectIter = insertLevel(selectKey); + ret.m_SelectIter = this->insertLevel(selectKey); ret.m_SelectIterEnd = this->m_SelectMap.end(); ret.m_LevelIter = ret.m_SelectIter->second.insert(value); return ret; --- a/c++/src/serial/stdtypes.cpp +++ b/c++/src/serial/stdtypes.cpp @@ -720,7 +720,7 @@ if ( IsSigned() ) { // signed -> unsigned // check for negative value - if ( IsNegative(value) ) + if ( CParent::IsNegative(value) ) ThrowIntegerOverflow(); } if ( sizeof(value) > sizeof(result) ) { @@ -751,7 +751,7 @@ // unsigned -> signed if ( sizeof(value) == sizeof(result) ) { // same size - check for sign change only - if ( IsNegative(result) ) + if ( CParent::IsNegative(result) ) ThrowIntegerOverflow(); } } @@ -786,7 +786,7 @@ if ( IsSigned() ) { // signed -> unsigned // check for negative value - if ( IsNegative(value) ) + if ( CParent::IsNegative(value) ) ThrowIntegerOverflow(); } if ( sizeof(value) > sizeof(result) ) { @@ -817,7 +817,7 @@ // unsigned -> signed if ( sizeof(value) == sizeof(result) ) { // same size - check for sign change only - if ( IsNegative(result) ) + if ( CParent::IsNegative(result) ) ThrowIntegerOverflow(); } } debian/patches/series0000644000000000000000000000021512152773066012041 0ustar enable_clean_after_failed_compile hurd_fixes legacy_rename_rpsblast fix_lib_deps no_multiarch_rpath use_pie_for_apps skip_services_unit_test debian/patches/use_pie_for_apps0000644000000000000000000000234412152774743014101 0ustar Subject: build executables with -fPIE, not -fPIC * -fPIC is only useful for shared libraries; substitute -fPIE (along with -pie at link time) when building executables. Author: Aaron M. Ucko Last-Update: 2012-05-10 --- a/c++/src/build-system/Makefile.app.in +++ b/c++/src/build-system/Makefile.app.in @@ -24,8 +24,8 @@ default_rule: all ### C/C++ source file compilation (and maybe auto-dependencies) build rules -CXXFLAGS_ALL = @f_compile@ $(CXXFLAGS) $(LOCAL_CPPFLAGS) $(CPPFLAGS) -CFLAGS_ALL = @f_compile@ $(CFLAGS) $(LOCAL_CPPFLAGS) $(CPPFLAGS) +CXXFLAGS_ALL = @f_compile@ $(CXXFLAGS:-fPIC=-fPIE) $(LOCAL_CPPFLAGS) $(CPPFLAGS) +CFLAGS_ALL = @f_compile@ $(CFLAGS:-fPIC=-fPIE) $(LOCAL_CPPFLAGS) $(CPPFLAGS) SOURCES = @UNIX_SRC@ $(SRC) include $(builddir)/Makefile.$(Rules) @@ -72,7 +72,7 @@ rebuild-libs: $(XAPP): $(XOBJ) $(XLIBDEP) @-$(RM) .$(XAPP).stamp - $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) $(XOBJ) $(XOBJ2) $(PRE_LIBS) $(XLIB) $(XAPP_LIBS) @f_outexe@$(XAPP) $(LINK_FILTER) + $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) -fPIE -pie $(XOBJ) $(XOBJ2) $(PRE_LIBS) $(XLIB) $(XAPP_LIBS) @f_outexe@$(XAPP) $(LINK_FILTER) $(STRIP) $(XAPP) $(POST_LINK) $(XAPP) ifneq "$(BINCOPY)" "@:" debian/patches/fix_gcc46_errors0000644000000000000000000000162611570464731013725 0ustar Subject: GCC 4.6 compilation error due to missing def * include/corelib/ncbistre.hpp: Add stddef definition required by gcc4.6 * src/objtools/blast/seqdb_reader/seqdbimpl.hpp: remove mutable reference Author: Olivier Sallou Last-Update: 2011-05-03 --- a/c++/include/corelib/ncbistre.hpp +++ b/c++/include/corelib/ncbistre.hpp @@ -116,6 +116,7 @@ #define SEEKOFF PUBSEEKOFF #include +#include // (BEGIN_NCBI_SCOPE must be followed by END_NCBI_SCOPE later in this file) --- a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp +++ b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp @@ -1245,7 +1245,7 @@ CSeqDBAtlasHolder m_AtlasHolder; /// Reference to memory management layer. - mutable CSeqDBAtlas & m_Atlas; + CSeqDBAtlas & m_Atlas; /// The list of database names provided to the constructor. string m_DBNames; debian/patches/skip_services_unit_test0000644000000000000000000000111112152773066015512 0ustar Subject: remove network required test Author: Tim Booth Forwarded: no Description: test require internet connection Last-Updated: 2013-06-01 --- a/c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app +++ b/c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app @@ -11,6 +11,7 @@ LIBS = $(NETWORK_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(ORIG_LIBS) -CHECK_CMD = blast_services_unit_test +# This test requires an internet connection, shouldn't be run on a build server +# CHECK_CMD = blast_services_unit_test WATCHERS = madden camacho debian/patches/enable_clean_after_failed_compile0000644000000000000000000000071112152773066017335 0ustar Subject: clean after failure Description: Enable clean Author: Tim Booth Last-Updated: 2013-06-01 Forwarded: no --- a/c++/src/build-system/new_module.sh.in +++ b/c++/src/build-system/new_module.sh.in @@ -178,7 +178,7 @@ if test -x "$bindir/datatool"; then datatool=$bindir/datatool COMMON_AddRunpath "$libdir" - else + elif [ "$1" != "purge_sources" ] ; then echo "Unable to find datatool." >&2 exit 2 fi debian/patches/do_not_output_everything_to_stderr.patch0000644000000000000000000000337311742121460021075 0ustar Author: Andreas Tille Date: Wed, 21 Dec 2011 15:47:04 +0100 Bug-Closed: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644237 Description: Output non-erroneous messages to STDOUT instead of STDERR --- ncbi-blast+-2.2.25.orig/c++/src/app/blast/update_blastdb.pl +++ ncbi-blast+-2.2.25/c++/src/app/blast/update_blastdb.pl @@ -104,7 +104,7 @@ or die "Failed to login to " . NCBI_FTP . ": $!\n"; $ftp->cwd(BLAST_DB_DIR); $ftp->binary(); - print STDERR "Connected to NCBI\n" if $opt_verbose; + print STDOUT "Connected to NCBI\n" if $opt_verbose; return $ftp; } @@ -170,14 +170,14 @@ if ($opt_verbose and &is_multivolume_db($file)) { my $db_name = &extract_db_name($file); my $nvol = &get_num_volumes($db_name, @_); - print STDERR "Downloading $db_name (" . $nvol . " volumes) ...\n"; + print STDOUT "Downloading $db_name (" . $nvol . " volumes) ...\n"; } download_file: if ($opt_force_download or not -f $file or ((stat($file))->mtime < $ftp->mdtm($file))) { - print STDERR "Downloading $file... " if $opt_verbose; + print STDOUT "Downloading $file... " if $opt_verbose; $ftp->get($file); if ($opt_check_md5) { unless ($ftp->get("$file.md5")) { @@ -199,10 +199,10 @@ } } } - print STDERR "done.\n" if $opt_verbose; + print STDOUT "done.\n" if $opt_verbose; $retval = 1 if ($retval == 0); } else { - print STDERR "$file is up to date.\n" if $opt_verbose; + print STDOUT "$file is up to date.\n" if $opt_verbose; } } return $retval; debian/patches/hurd_fixes0000644000000000000000000000341612152773066012715 0ustar Subject: fix portability issues that led to Hurd build failures * src/build-system/configure(.ac): - Reflect the Hurd's support for -Wl,rpath,... . * src/connect/ncbi_socket_cxx.cpp, src/connect/ext/ncbi_localnet.c: cope with missing PATH_MAX everywhere, not just under Windows. Author: Aaron M. Ucko Last-Update: 2011-06-10 --- a/c++/src/build-system/configure +++ b/c++/src/build-system/configure @@ -5860,7 +5860,7 @@ solaris* ) CONF_f_runpath="-R" ;; - linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC ) + linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC | gnu*:GCC ) CONF_f_runpath="-Wl,-rpath," ;; linux*:ICC ) --- a/c++/src/build-system/configure.ac +++ b/c++/src/build-system/configure.ac @@ -1558,7 +1558,7 @@ solaris* ) CONF_f_runpath="-R" ;; - linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC ) + linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC | gnu*:GCC ) CONF_f_runpath="-Wl,-rpath," ;; linux*:ICC ) --- a/c++/src/connect/ncbi_socket_cxx.cpp +++ b/c++/src/connect/ncbi_socket_cxx.cpp @@ -35,7 +35,7 @@ #include "ncbi_assert.h" // no _ASSERT()s, keep clean from xncbi #include #include // for PATH_MAX -#if defined(NCBI_OS_MSWIN) && !defined(PATH_MAX) +#ifndef PATH_MAX # define PATH_MAX 512 // will actually use less than 32 chars #endif // NCBI_OS_MSWIN && !PATH_MAX --- a/c++/src/connect/ext/ncbi_localnet.c +++ b/c++/src/connect/ext/ncbi_localnet.c @@ -62,6 +62,10 @@ # endif /*_MAX_PATH*/ #endif /*NCBI_OS_MSWIN && !PATH_MAX*/ +#if !defined(PATH_MAX) +# define PATH_MAX 4096 +#endif /*Patch added for Ubuntu build*/ + #if PATH_MAX < 256 # define BUFSIZE 256 #else debian/source/0000755000000000000000000000000012153003406010460 5ustar debian/source/format0000644000000000000000000000001411570234561011700 0ustar 3.0 (quilt) debian/docs0000644000000000000000000000000011570234561010033 0ustar