From 66c4803f14169d4a8bf2f92e84d42f5776fe4fed Mon Sep 17 00:00:00 2001 From: Andreas Tille Date: Wed, 21 Dec 2011 16:44:13 +0000 Subject: [PATCH] Patch for more sensible output of a perl script; Depends python (as needed by a python script); DEP5 fixes --- debian/changelog | 12 ++++++ debian/control | 2 +- debian/copyright | 25 ++++------- .../do_not_output_everything_to_stderr.patch | 41 +++++++++++++++++++ debian/patches/series | 1 + 5 files changed, 64 insertions(+), 17 deletions(-) create mode 100644 debian/patches/do_not_output_everything_to_stderr.patch diff --git a/debian/changelog b/debian/changelog index e34dc2ba..53a99bfb 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,15 @@ +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: diff --git a/debian/control b/debian/control index 46ddc042..cdaae40e 100644 --- a/debian/control +++ b/debian/control @@ -14,7 +14,7 @@ Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-bla Package: ncbi-blast+ Architecture: any Enhances: t-coffee -Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, ${python:Depends}, ncbi-data +Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, python, ncbi-data Multi-Arch: foreign Description: next generation suite of BLAST sequence search tools The Basic Local Alignment Search Tool (BLAST) is the most widely diff --git a/debian/copyright b/debian/copyright index 5f6f51ed..656d0a9d 100644 --- a/debian/copyright +++ b/debian/copyright @@ -22,26 +22,23 @@ License: Files: c++/*/util/regexp/* Copyright: 1997-2009 University of Cambridge -2008-2009 Google Inc + 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 @@ -62,19 +59,16 @@ License: BSD 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 @@ -109,14 +103,14 @@ License: Boost software license 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 @@ -149,7 +143,7 @@ License: MIT 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. @@ -163,14 +157,14 @@ 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 @@ -178,7 +172,7 @@ License: PD 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/* @@ -199,4 +193,3 @@ License: GPL-2+ . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". - diff --git a/debian/patches/do_not_output_everything_to_stderr.patch b/debian/patches/do_not_output_everything_to_stderr.patch new file mode 100644 index 00000000..f51509d6 --- /dev/null +++ b/debian/patches/do_not_output_everything_to_stderr.patch @@ -0,0 +1,41 @@ +--- 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; diff --git a/debian/patches/series b/debian/patches/series index 51dcf9df..6028e8dd 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -5,3 +5,4 @@ fix_gcc46_errors support_other_cpus fix_lib_deps no_multiarch_rpath +do_not_output_everything_to_stderr.patch -- 2.30.2