[med-svn] [SCM] emboss branch, master, updated. debian/6.3.1-6-15-g0183966
Charles Plessy
plessy at debian.org
Fri May 11 05:15:08 UTC 2012
The following commit has been merged in the master branch:
commit 01839666b934ef57f0d4fe7f4fd91cc20a727c6e
Author: Charles Plessy <plessy at debian.org>
Date: Fri May 11 13:36:59 2012 +0900
Machine-readable Debian copyright file, concluding that the UniProt records are not copyrighted.
See: http://lists.debian.org/20120509035346.GA313@falafel.plessy.net
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..32fc726
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,201 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.4.0.tar.gz
+
+Files: *
+Copyright: The EMBOSS developers or their employers.
+License: emboss
+ EMBOSS License (http://emboss.sourceforge.net/licence/)
+ .
+ The AJAX and NUCLEUS libraries are released under the GNU Library General
+ Public Licence.
+ .
+ The EMBOSS Administrator’s Guide can be copied, distributed and/or modified
+ under the terms of the GNU Free Documentation License, Version 1.1 or any
+ later version published by the Free Software Foundation; with no Invariant
+ Sections, with no Front-Cover Texts, and with no Back-Cover Texts. A copy of
+ the license is included in the chapter entitled ”GNU Free Documentation
+ License”.
+ .
+ The EMBOSS Quick Guide has been relicenced and can be used, modified and
+ distributed under the same terms as EMBOSS itself.
+ .
+ EMBOSS applications are released under the GNU General Public Licence.
+ .
+ Parsing of ACD files does not constitute a "derived work" and developers are
+ encouraged to do this, for example to write their own GUIs.
+ .
+ For developers who have their own licensing conditions already in effect, there
+ will be an additional way to contribute. The EMBASSY collection can include
+ packages that use the EMBOSS core libraries and interfaces but under their own
+ licensing conditions. They will be bound by the Library GPL of the AJAX and
+ NUCLEUS libraries, but not necessarily by the full GPL.
+ .
+ Some of the suggestions and code examples from David Hanson's book
+ "C Interfaces and Implementations" are included in the AJAX library.
+ This library is available from http://www.cs.princeton.edu/software/cii/
+ or ftp://ftp.cs.princeton.edu/pub/packages/cii/
+ .
+ The COPYRIGHT file in release 1.10 says:
+ .
+ > The author of this software is David R. Hanson.
+ >
+ > Copyright (c) 1994,1995,1996 by David R. Hanson. All Rights Reserved.
+ >
+ > Permission to use, copy, modify, and distribute this software for any
+ > purpose, subject to the provisions described below, without fee is
+ > hereby granted, provided that this entire notice is included in all
+ > copies of any software that is or includes a copy or modification of
+ > this software and in all copies of the supporting documentation for
+ > such software.
+ >
+ > THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR IMPLIED
+ > WARRANTY. IN PARTICULAR, THE AUTHOR DOES MAKE ANY REPRESENTATION OR
+ > WARRANTY OF ANY KIND CONCERNING THE MERCHANTABILITY OF THIS SOFTWARE OR
+ > ITS FITNESS FOR ANY PARTICULAR PURPOSE.
+ >
+ > David Hanson / drh at cs.princeton.edu / http://www.cs.princeton.edu/~drh/
+ > Wed Apr 24 13:44:16 PDT 1996
+ > Mon Dec 12 15:58:13 EST 1994
+Comment: On Debian systems, the complete text of the GNU General Public License
+ version 2, the GNU Free Documentation License version 1.2, and the GNU Library
+ Public License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’,
+ ‘/usr/share/common-licenses/GFDL-1.2’ and ‘/usr/share/common-licenses/LGPL-2’
+ respectively.
+
+Files: ajax/pcre/*
+Copyright: © 1997-2000 University of Cambridge
+License: PCRE
+ PCRE is a library of functions to support regular expressions whose syntax
+ and semantics are as close as possible to those of the Perl 5 language.
+ .
+ Written by: Philip Hazel <ph10 at cam.ac.uk>
+ .
+ University of Cambridge Computing Service,
+ Cambridge, England. Phone: +44 1223 334714.
+ .
+ Copyright (c) 1997-2000 University of Cambridge
+ .
+ Permission is granted to anyone to use this software for any purpose on any
+ computer system, and to redistribute it freely, subject to the following
+ restrictions:
+ .
+ 1. This software 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.
+ .
+ 2. The origin of this software must not be misrepresented, either by
+ explicit claim or by omission. In practice, this means that if you use
+ PCRE in software which you distribute to others, commercially or
+ otherwise, you must put a sentence like this
+ .
+ Regular expression support is provided by the PCRE library package,
+ which is open source software, written by Philip Hazel, and copyright
+ by the University of Cambridge, England.
+ .
+ somewhere reasonably visible in your documentation and in any relevant
+ files or online help data or similar. A reference to the ftp site for
+ the source, that is, to
+ .
+ ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/
+ .
+ should also be given in the documentation.
+ .
+ 3. Altered versions must be plainly marked as such, and must not be
+ misrepresented as being the original software.
+ .
+ 4. If PCRE is embedded in any software that is released under the GNU
+ General Purpose Licence (GPL), then the terms of that licence shall
+ supersede any condition above with which it is incompatible.
+
+Files: plplot/*
+Copyright: © 1987, 1988 by Digital Equipment Corporation, Maynard, Massachusetts,
+ © 1991, 1993, 1994 Wesley Ebisuzaki
+ © 1992, 1993, 1994, 1995, 2001, 2002, 2004 Maurice LeBrun
+ © 1992, 1999, 2001 Geoffrey Furnish
+ © 1992, Maurice J. LeBrun, Geoff Furnish, Tony Richardson.
+ © 2000, 2001, 2002, 2004, 2005 Alan W. Irwin
+ © 2000, 2001, 2002, 2003, 2004 Joao Cardoso
+ © 2001, 2003, 2004, 2005 Rafael Laboissiere
+ © 2001, 2002, 2003, 2004 Andrew Roach
+ © 2002, Vincent Darley
+ © 2004, 2005 Thomas J. Duck
+ © 2004, 2005, 2006 Andrew Ross
+ © 2006, Hazen Babcock
+ © 2006, Jim Dishaw
+ © 2006, Werner Smekal
+License: GPL-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 Library General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc. 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Files: ajax/zlib/*
+Copyright: © 1995-2005 Jean-loup Gailly and Mark Adler
+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.
+ .
+ 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.
+ .
+ Jean-loup Gailly Mark Adler
+ jloup at gzip.org madler at alumni.caltech.edu
+
+Files: doc/programs/html/antigenic.html
+ doc/programs/html/pasteseq.html
+ doc/programs/html/showpep.html
+ doc/programs/master/emboss/apps/inc/acdc.input
+ doc/programs/master/emboss/apps/inc/acdlog.input
+ doc/programs/master/emboss/apps/inc/acdtrace.input
+ doc/programs/master/emboss/apps/inc/antigenic.input
+ doc/programs/master/emboss/apps/inc/pasteseq.input
+ doc/programs/master/emboss/apps/inc/showpep.input
+ doc/programs/text/antigenic.txt
+ doc/programs/text/pasteseq.txt
+ doc/programs/text/showpep.txt
+ emboss/data/dbxref.txt
+ test/data/amir.swiss
+ test/data/uniprotft.sw
+ test/swiss/seq.dat
+ test/swnew/trembl.dat
+Copyright: none
+ These files are marked to be copyrighted by the UniProt Consortium, but this
+ applies to the UniProt database as a whole, not to the individual records.
+License: not-the-CC-BY-ND-3.0
+ Despite the following statement:
+ .
+ Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
+ Distributed under the Creative Commons Attribution-NoDerivs License
+ .
+ The above files, as individual records, are not copyrighted. The statement is
+ for the UniProt as a whole.
+
+Files: debian/*
+Copyright: the developers
+License: unclear
+ The EMBOSS package for Debian was initially prepared by Matt Hope
+ (dopey at debian.org) in 2002-2004 and released on
+ (http://debian.bioinformatics.unsw.edu.au/). The package distributed in Debian
+ was prepared by the "pkg-emboss" project in 2006, using the work of Matt Hope
+ as a starting point. The packaging work of the pkg-emboss project is in the
+ public domain unless stated otherwise.
+
diff --git a/debian/copyright.introduction b/debian/copyright.introduction
deleted file mode 100644
index 6b4c3c1..0000000
--- a/debian/copyright.introduction
+++ /dev/null
@@ -1,190 +0,0 @@
-Source: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.4.0.tar.gz
-
-------------------------------------------------------------------------
-EMBOSS License (http://emboss.sourceforge.net/licence/)
-
-The AJAX and NUCLEUS libraries are released under the GNU Library General
-Public Licence.
-
-The EMBOSS Administrator’s Guide can be copied, distributed and/or modified
-under the terms of the GNU Free Documentation License, Version 1.1 or any
-later version published by the Free Software Foundation; with no Invariant
-Sections, with no Front-Cover Texts, and with no Back-Cover Texts. A copy of
-the license is included in the chapter entitled ”GNU Free Documentation
-License”.
-
-The EMBOSS Quick Guide has been relicenced and can be used, modified and
-distributed under the same terms as EMBOSS itself.
-
-EMBOSS applications are released under the GNU General Public Licence.
-
-Parsing of ACD files does not constitute a "derived work" and developers are
-encouraged to do this, for example to write their own GUIs.
-
-For developers who have their own licensing conditions already in effect, there
-will be an additional way to contribute. The EMBASSY collection can include
-packages that use the EMBOSS core libraries and interfaces but under their own
-licensing conditions. They will be bound by the Library GPL of the AJAX and
-NUCLEUS libraries, but not necessarily by the full GPL.
-------------------------------------------------------------------------
-
-On Debian systems, the complete text of the GNU General Public License version
-2, the GNU Free Documentation License version 1.2, and the GNU Library Public
-License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’,
-‘/usr/share/common-licenses/GFDL-1.2’ and ‘/usr/share/common-licenses/LGPL-2’
-respectively.
-
-
-EMBOSS uses the libpcre and libplplot.
-
-
-PCRE LICENCE
-------------
-
-PCRE is a library of functions to support regular expressions whose syntax
-and semantics are as close as possible to those of the Perl 5 language.
-
-Written by: Philip Hazel <ph10 at cam.ac.uk>
-
-University of Cambridge Computing Service,
-Cambridge, England. Phone: +44 1223 334714.
-
-Copyright (c) 1997-2000 University of Cambridge
-
-Permission is granted to anyone to use this software for any purpose on any
-computer system, and to redistribute it freely, subject to the following
-restrictions:
-
-1. This software 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.
-
-2. The origin of this software must not be misrepresented, either by
- explicit claim or by omission. In practice, this means that if you use
- PCRE in software which you distribute to others, commercially or
- otherwise, you must put a sentence like this
-
- Regular expression support is provided by the PCRE library package,
- which is open source software, written by Philip Hazel, and copyright
- by the University of Cambridge, England.
-
- somewhere reasonably visible in your documentation and in any relevant
- files or online help data or similar. A reference to the ftp site for
- the source, that is, to
-
- ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/
-
- should also be given in the documentation.
-
-3. Altered versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
-
-4. If PCRE is embedded in any software that is released under the GNU
- General Purpose Licence (GPL), then the terms of that licence shall
- supersede any condition above with which it is incompatible.
-
-
-PLPLOT LICENCE
---------------
-
-The PLplot package may be distributed under the following terms:
-
- 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 Library General Public
- License along with this library; if not, write to the Free Software
- Foundation, Inc. 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
-
-ZLIB LICENSE
-------------
-
- Copyright (C) 1995-2005 Jean-loup Gailly and Mark Adler
-
- 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.
-
- Jean-loup Gailly Mark Adler
- jloup at gzip.org madler at alumni.caltech.edu
-
-
-(NOT SO) NON-FREE DATA IN THE TEST SUITE AND THE EXAMPLES ?
------------------------------------------------------------
-
-Files : doc/programs/html/antigenic.html
- doc/programs/html/pasteseq.html
- doc/programs/html/showpep.html
- doc/programs/master/emboss/apps/inc/acdc.input
- doc/programs/master/emboss/apps/inc/acdlog.input
- doc/programs/master/emboss/apps/inc/acdtrace.input
- doc/programs/master/emboss/apps/inc/antigenic.input
- doc/programs/master/emboss/apps/inc/pasteseq.input
- doc/programs/master/emboss/apps/inc/showpep.input
- doc/programs/text/antigenic.txt
- doc/programs/text/pasteseq.txt
- doc/programs/text/showpep.txt
- emboss/data/dbxref.txt
- test/data/amir.swiss
- test/data/uniprotft.sw
- test/swiss/seq.dat
- test/swnew/trembl.dat
-Copyright: UniProt Consortium
-License: CC-BY-ND-3.0
- Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
- Distributed under the Creative Commons Attribution-NoDerivs License
-Comment: Four comments:
- 1) The version number of CC-BY-ND was dertermined according to the URL that
- is included in ‘http://www.uniprot.org/terms’.
- .
- 2) The same page also links to ‘http://sciencecommons.org/resources/faq/databases/’,
- which contains arguments that the files documented in this paragraph are not
- copyrightable. While this remains to be confirmed, I will give them the benefit
- of the doubt for the moment. See ‘http://lists.debian.org/20110720013742.GB4831@merveille.plessy.net’
- for more discussion on the subject -- CP, Wed Jul 20, 2011
- .
- 3) Found with ‘git grep 'Copyrighted by the UniProt Consortium' | cut -f1 -d':' | sort -u’
- .
- 4) The documentation files contain full copies of UniProt records as
- examples of input, and therefore are not false positives.
-
-
-DEBIAN PACKAGING
-----------------
-
-The EMBOSS package for Debian was initially prepared by Matt Hope
-(dopey at debian.org) in 2002-2004 and released on
-(http://debian.bioinformatics.unsw.edu.au/). The package distributed in Debian
-was prepared by the "pkg-emboss" project in 2006, using the work of Matt Hope
-as a starting point. The packaging work of the pkg-emboss project is in the
-public domain unless stated otherwise.
-
-
-AUTHORS OF EMBOSS
------------------
-
-EMBOSS has been develped by many programmers, who are acknowledged it the
-AUTHORS and THANK files in the original sources. These two files are reproduced
-below:
-
-
diff --git a/debian/rules b/debian/rules
index 83e994c..b281e57 100755
--- a/debian/rules
+++ b/debian/rules
@@ -32,7 +32,7 @@ config.status:
include /usr/share/quilt/quilt.make
-build: config.status patch debian/copyright build-stamp
+build: config.status patch build-stamp
build-stamp:
dh_testdir
$(MAKE) AJAX_FIXED_ROOT=\\\"/usr/share/EMBOSS\\\" LDFLAGS="$(DEB_LDFLAGS)"
@@ -44,11 +44,6 @@ debian/manpages/success:
debian/build-manpages.sh
echo "The manpages have been sucessfully built" > debian/manpages/success
-debian/copyright:
- cat debian/copyright.introduction > $@
- cat "AUTHORS" >> $@
- cat "THANKS" >> $@
-
clean: unpatch
dh_testdir
dh_testroot
--
The European Molecular Biology Open Software Suite.
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