[med-svn] r17657 - in trunk/packages/infernal/tags: . 1.1.1-1/debian
Charles Plessy
plessy at moszumanska.debian.org
Fri Aug 8 13:16:57 UTC 2014
Author: plessy
Date: 2014-08-08 13:16:56 +0000 (Fri, 08 Aug 2014)
New Revision: 17657
Added:
trunk/packages/infernal/tags/1.1.1-1/
trunk/packages/infernal/tags/1.1.1-1/debian/changelog
trunk/packages/infernal/tags/1.1.1-1/debian/control
trunk/packages/infernal/tags/1.1.1-1/debian/copyright
Removed:
trunk/packages/infernal/tags/1.1.1-1/debian/changelog
trunk/packages/infernal/tags/1.1.1-1/debian/control
trunk/packages/infernal/tags/1.1.1-1/debian/copyright
Log:
[svn-buildpackage] Tagging infernal 1.1.1-1
Deleted: trunk/packages/infernal/tags/1.1.1-1/debian/changelog
===================================================================
--- trunk/packages/infernal/trunk/debian/changelog 2014-08-07 16:14:07 UTC (rev 17634)
+++ trunk/packages/infernal/tags/1.1.1-1/debian/changelog 2014-08-08 13:16:56 UTC (rev 17657)
@@ -1,132 +0,0 @@
-infernal (1.1~rc4-3) UNRELEASED; urgency=low
-
- * Removed i386 architecture as some processors do not provide SSE2.
-
- -- Charles Plessy <plessy at debian.org> Sat, 05 Oct 2013 09:48:09 +0900
-
-infernal (1.1~rc4-2) unstable; urgency=low
-
- * Team upload.
- * Build-depends on libperl4-corelibs-perl (Closes: #724119).
- * debian/control: removed myself from Uploaders.
-
- -- Charles Plessy <plessy at debian.org> Mon, 23 Sep 2013 10:57:17 +0900
-
-infernal (1.1~rc4-1) unstable; urgency=low
-
- * New upstream source
- * debian/source/format: 3.0 (quilt)
- * debian/control:
- - cme fix dpkg-control
- - debhelper 9
- - do not Build-Depend: quilt since source format implies this
- - The package builds only on architectures with SSE instructions.
- Quoting from build log on armel:
- configure: WARNING: Infernal 1.1 requires VMX or SSE capability for
- parallel instructions.
- configure: error: It appears your platform has neither and will not
- support Infernal.
- So all non i386/amd64 architectures were excluded
- Closes: #718742
- - use anonscm in Vcs fields
- * debian/rules:
- - remove redundant setting for flags which is handled by debhelper 9
- automatically
- - use xz compression
- * debian/copyright: DEP5
-
- -- Andreas Tille <tille at debian.org> Mon, 05 Aug 2013 12:06:12 +0200
-
-infernal (1.1~rc2-1) unstable; urgency=low
-
- * New upstream version - aiming to support RNAWorld BOINC project,
- with many thanks and regards to Yoyo!
- - cmscore no longer available
- * Bumped policy to 3.9.4 (no changes needed)
- - introduced hardening, with it build dep on
- dpkg-dev (>= 1.16.1~)
-
- -- Steffen Moeller <moeller at debian.org> Wed, 01 May 2013 20:24:17 +0200
-
-infernal (1.0.2-3) UNRELEASED; urgency=low
-
- [ Steffen Moeller ]
- * Extra fixed for lintian cleanliness (Steffen)
-
- [ Andreas Tille ]
- * debian/upstream:
- - do not specify DOI twice
- - Moved PMID to references
- * debian/control:
- - Fixed Vcs-Svn field
- - Standards-Version: 3.9.3 (no changes needed)
-
- -- Andreas Tille <tille at debian.org> Thu, 08 Mar 2012 11:44:54 +0100
-
-infernal (1.0.2-2) unstable; urgency=low
-
- * Series of mall fixes (Closes: #643407).
- * source/format 3.0
- * Policy to 3.9.2
- * added infernal-dbg
- * corrected upstream's email address
-
- -- Steffen Moeller <moeller at debian.org> Tue, 27 Sep 2011 15:48:27 +0200
-
-infernal (1.0.2-1) unstable; urgency=low
-
- * New upstream version
-
- -- Andreas Tille <tille at debian.org> Tue, 03 Nov 2009 11:15:34 +0100
-
-infernal (1.0-2) unstable; urgency=low
-
- * Switch to CDBS to benefit from automagical config.{sub,guess}
- update (debian/rules). Closes: #550253.
- * debian/control:
- - Depend on cdbs, downgraded requirement on debhelper from 7.1 to 7.
- - Transferred bibliographic information from the package description
- to debian/upstream-metadata.yaml.
- - Clarified the short description of the documentation package.
- * Removed debian/infernal.dirs, not needed.
- * Edited README.source, removing mention that infernal is in contrib.
- * debian/copyright points at the version 3 of the GPL.
-
- -- Charles Plessy <plessy at debian.org> Sat, 10 Oct 2009 11:22:35 +0900
-
-infernal (1.0-1) unstable; urgency=low
-
- [ Charles Plessy ]
- * Updated my email address.
-
- [ Andreas Tille ]
- * New upstream version
- * debian/control:
- - Standards-Version: 3.8.3 (no changes needed)
- - Added myself to uploaders
- - s/Debian-Med/Debian Med/
- - Build-Depends: debhelper (>= 7.1) autotools-dev
- - Package: infernal-doc
- * debian/rules rewritten to make use of short dh
- * debian/copyright:
- - added myself to Copyright holders of debian/*
- - squid is not part of the upstream tarball anymore so this
- paragraph was deleted
- - files/Userguide.pdf: Copied comment about PDF = source from
- README.Debian
- * debian/infernal-doc.doc-base
- * debian/infernal.install: install src/{trcyk,truncyk_check} to
- /usr/bin
-
- * TODO: Convince upstream to release libeazel which is also used in
- hmmer as a separate library instead of copying the code into
- different projects
-
- -- Andreas Tille <tille at debian.org> Fri, 25 Sep 2009 15:17:22 +0200
-
-infernal (0.81-1) experimental; urgency=low
-
- * Initial release (Closes: #441840)
-
- -- Steffen Moeller <moeller at debian.org> Mon, 10 Sep 2007 23:15:37 +0200
-
Copied: trunk/packages/infernal/tags/1.1.1-1/debian/changelog (from rev 17656, trunk/packages/infernal/trunk/debian/changelog)
===================================================================
--- trunk/packages/infernal/tags/1.1.1-1/debian/changelog (rev 0)
+++ trunk/packages/infernal/tags/1.1.1-1/debian/changelog 2014-08-08 13:16:56 UTC (rev 17657)
@@ -0,0 +1,142 @@
+infernal (1.1.1-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream release.
+
+ -- Charles Plessy <plessy at debian.org> Fri, 08 Aug 2014 21:45:26 +0900
+
+infernal (1.1-1) unstable; urgency=low
+
+ * Team upload.
+ * New upstream release.
+ * Removed i386 architecture as some processors do not provide SSE2.
+ * Conforms with Policy 3.9.5.
+
+ -- Charles Plessy <plessy at debian.org> Sun, 01 Dec 2013 10:30:00 +0900
+
+infernal (1.1~rc4-2) unstable; urgency=low
+
+ * Team upload.
+ * Build-depends on libperl4-corelibs-perl (Closes: #724119).
+ * debian/control: removed myself from Uploaders.
+
+ -- Charles Plessy <plessy at debian.org> Mon, 23 Sep 2013 10:57:17 +0900
+
+infernal (1.1~rc4-1) unstable; urgency=low
+
+ * New upstream source
+ * debian/source/format: 3.0 (quilt)
+ * debian/control:
+ - cme fix dpkg-control
+ - debhelper 9
+ - do not Build-Depend: quilt since source format implies this
+ - The package builds only on architectures with SSE instructions.
+ Quoting from build log on armel:
+ configure: WARNING: Infernal 1.1 requires VMX or SSE capability for
+ parallel instructions.
+ configure: error: It appears your platform has neither and will not
+ support Infernal.
+ So all non i386/amd64 architectures were excluded
+ Closes: #718742
+ - use anonscm in Vcs fields
+ * debian/rules:
+ - remove redundant setting for flags which is handled by debhelper 9
+ automatically
+ - use xz compression
+ * debian/copyright: DEP5
+
+ -- Andreas Tille <tille at debian.org> Mon, 05 Aug 2013 12:06:12 +0200
+
+infernal (1.1~rc2-1) unstable; urgency=low
+
+ * New upstream version - aiming to support RNAWorld BOINC project,
+ with many thanks and regards to Yoyo!
+ - cmscore no longer available
+ * Bumped policy to 3.9.4 (no changes needed)
+ - introduced hardening, with it build dep on
+ dpkg-dev (>= 1.16.1~)
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 01 May 2013 20:24:17 +0200
+
+infernal (1.0.2-3) UNRELEASED; urgency=low
+
+ [ Steffen Moeller ]
+ * Extra fixed for lintian cleanliness (Steffen)
+
+ [ Andreas Tille ]
+ * debian/upstream:
+ - do not specify DOI twice
+ - Moved PMID to references
+ * debian/control:
+ - Fixed Vcs-Svn field
+ - Standards-Version: 3.9.3 (no changes needed)
+
+ -- Andreas Tille <tille at debian.org> Thu, 08 Mar 2012 11:44:54 +0100
+
+infernal (1.0.2-2) unstable; urgency=low
+
+ * Series of mall fixes (Closes: #643407).
+ * source/format 3.0
+ * Policy to 3.9.2
+ * added infernal-dbg
+ * corrected upstream's email address
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 27 Sep 2011 15:48:27 +0200
+
+infernal (1.0.2-1) unstable; urgency=low
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Tue, 03 Nov 2009 11:15:34 +0100
+
+infernal (1.0-2) unstable; urgency=low
+
+ * Switch to CDBS to benefit from automagical config.{sub,guess}
+ update (debian/rules). Closes: #550253.
+ * debian/control:
+ - Depend on cdbs, downgraded requirement on debhelper from 7.1 to 7.
+ - Transferred bibliographic information from the package description
+ to debian/upstream-metadata.yaml.
+ - Clarified the short description of the documentation package.
+ * Removed debian/infernal.dirs, not needed.
+ * Edited README.source, removing mention that infernal is in contrib.
+ * debian/copyright points at the version 3 of the GPL.
+
+ -- Charles Plessy <plessy at debian.org> Sat, 10 Oct 2009 11:22:35 +0900
+
+infernal (1.0-1) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * Updated my email address.
+
+ [ Andreas Tille ]
+ * New upstream version
+ * debian/control:
+ - Standards-Version: 3.8.3 (no changes needed)
+ - Added myself to uploaders
+ - s/Debian-Med/Debian Med/
+ - Build-Depends: debhelper (>= 7.1) autotools-dev
+ - Package: infernal-doc
+ * debian/rules rewritten to make use of short dh
+ * debian/copyright:
+ - added myself to Copyright holders of debian/*
+ - squid is not part of the upstream tarball anymore so this
+ paragraph was deleted
+ - files/Userguide.pdf: Copied comment about PDF = source from
+ README.Debian
+ * debian/infernal-doc.doc-base
+ * debian/infernal.install: install src/{trcyk,truncyk_check} to
+ /usr/bin
+
+ * TODO: Convince upstream to release libeazel which is also used in
+ hmmer as a separate library instead of copying the code into
+ different projects
+
+ -- Andreas Tille <tille at debian.org> Fri, 25 Sep 2009 15:17:22 +0200
+
+infernal (0.81-1) experimental; urgency=low
+
+ * Initial release (Closes: #441840)
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 10 Sep 2007 23:15:37 +0200
+
Deleted: trunk/packages/infernal/tags/1.1.1-1/debian/control
===================================================================
--- trunk/packages/infernal/trunk/debian/control 2014-08-07 16:14:07 UTC (rev 17634)
+++ trunk/packages/infernal/tags/1.1.1-1/debian/control 2014-08-08 13:16:56 UTC (rev 17657)
@@ -1,61 +0,0 @@
-Source: infernal
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>,
- Andreas Tille <tille at debian.org>
-Section: science
-Priority: optional
-Build-Depends: dpkg-dev (>= 1.16.1~),
- debhelper (>= 9),
- libperl4-corelibs-perl,
- autotools-dev
-Standards-Version: 3.9.4
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/infernal/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/infernal/trunk/
-Homepage: http://infernal.janelia.org/
-
-Package: infernal
-Architecture: amd64 kfreebsd-amd64
-Depends: ${shlibs:Depends},
- ${misc:Depends}
-Description: inference of RNA secondary structural alignments
- Infernal ("INFERence of RNA ALignment") searches DNA sequence
- databases for RNA structure and sequence similarities. It provides an
- implementation of a special variant of profile stochastic context-free
- grammars called covariance models (CMs). A CM is like a sequence
- profile, but it scores a combination of sequence consensus and RNA
- secondary structure consensus, so in many cases, it is more capable of
- identifying RNA homologs that conserve their secondary structure more
- than their primary sequence.
- .
- The tool is an integral component of the Rfam database.
-
-Package: infernal-doc
-Architecture: all
-Section: doc
-Depends: ${shlibs:Depends},
- ${misc:Depends}
-Description: inference of RNA secondary structural alignments – documentation
- Infernal ("INFERence of RNA ALignment") searches DNA sequence
- databases for RNA structure and sequence similarities. It provides an
- implementation of a special case of profile stochastic context-free
- grammars called covariance models (CMs). A CM is like a sequence
- profile, but it scores a combination of sequence consensus and RNA
- secondary structure consensus, so in many cases, it is more capable of
- identifying RNA homologs that conserve their secondary structure more
- than their primary sequence.
- .
- This package provides the documentation which is shipped with the
- code of infernal.
-
-Package: infernal-dbg
-Architecture: amd64 kfreebsd-amd64
-Section: debug
-Priority: extra
-Depends: ${misc:Depends},
- infernal (= ${binary:Version})
-Description: debug information for infernal
- This package contains extra information to help the debugging of the
- infernal suite. The package is auto-generated. You may be asked
- by the upstream developer to install it to help the identification
- of a technical problem.
-
Copied: trunk/packages/infernal/tags/1.1.1-1/debian/control (from rev 17642, trunk/packages/infernal/trunk/debian/control)
===================================================================
--- trunk/packages/infernal/tags/1.1.1-1/debian/control (rev 0)
+++ trunk/packages/infernal/tags/1.1.1-1/debian/control 2014-08-08 13:16:56 UTC (rev 17657)
@@ -0,0 +1,61 @@
+Source: infernal
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: dpkg-dev (>= 1.16.1~),
+ debhelper (>= 9),
+ libperl4-corelibs-perl,
+ autotools-dev
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/infernal/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/infernal/trunk/
+Homepage: http://infernal.janelia.org/
+
+Package: infernal
+Architecture: amd64 kfreebsd-amd64
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: inference of RNA secondary structural alignments
+ Infernal ("INFERence of RNA ALignment") searches DNA sequence
+ databases for RNA structure and sequence similarities. It provides an
+ implementation of a special variant of profile stochastic context-free
+ grammars called covariance models (CMs). A CM is like a sequence
+ profile, but it scores a combination of sequence consensus and RNA
+ secondary structure consensus, so in many cases, it is more capable of
+ identifying RNA homologs that conserve their secondary structure more
+ than their primary sequence.
+ .
+ The tool is an integral component of the Rfam database.
+
+Package: infernal-doc
+Architecture: all
+Section: doc
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: inference of RNA secondary structural alignments – documentation
+ Infernal ("INFERence of RNA ALignment") searches DNA sequence
+ databases for RNA structure and sequence similarities. It provides an
+ implementation of a special case of profile stochastic context-free
+ grammars called covariance models (CMs). A CM is like a sequence
+ profile, but it scores a combination of sequence consensus and RNA
+ secondary structure consensus, so in many cases, it is more capable of
+ identifying RNA homologs that conserve their secondary structure more
+ than their primary sequence.
+ .
+ This package provides the documentation which is shipped with the
+ code of infernal.
+
+Package: infernal-dbg
+Architecture: amd64 kfreebsd-amd64
+Section: debug
+Priority: extra
+Depends: ${misc:Depends},
+ infernal (= ${binary:Version})
+Description: debug information for infernal
+ This package contains extra information to help the debugging of the
+ infernal suite. The package is auto-generated. You may be asked
+ by the upstream developer to install it to help the identification
+ of a technical problem.
+
Deleted: trunk/packages/infernal/tags/1.1.1-1/debian/copyright
===================================================================
--- trunk/packages/infernal/trunk/debian/copyright 2014-08-07 16:14:07 UTC (rev 17634)
+++ trunk/packages/infernal/tags/1.1.1-1/debian/copyright 2014-08-08 13:16:56 UTC (rev 17657)
@@ -1,144 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Contact: Infernal developer team at HHMI Janelia Farm:
- Diana Kolbe <kolbed janelia.hhmi.org>
- Eric Nawrocki <nawrockie janelia.hhmi.org>
- Sean Eddy <eddys janelia.hhmi.org>.
-Source: ftp://infernal.janelia.org/pub/software/infernal
-
-Files: debian/*
-Copyright: © 2007-2008 Steffen Moeller <moeller at debian.org>
- © 2007-2008 Charles Plessy <plessy at debian.org>
- © 2009-2013 Andreas Tille <tille at debian.org>
-License: GPL-3
-
-Files: rigfilters/*
-Copyright: © 2004, Zasha Weinberg
-License: BSD-like
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
- .
- - Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- - Redistributions in binary form must reproduce the above
- copyright notice, this list of conditions and the following
- disclaimer in the documentation and/or other materials provided
- with the distribution.
- - Neither the name of the University of Washington nor the names of
- its contributors may be used to endorse or promote products derived
- from this software without specific prior written permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
- NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
- FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
- SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
- INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
- SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
- HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
- STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
- IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-Files: easel/esl_sse.c easel/esl_vmx.c
-Copyright: © 2007 Julien Pommier
- © 1992 Stephen Moshier
-License: BSD-Easel
-
-Files: easel/easel.c::esl_tmpfile()
-Copyright: © 1999-2001 David A. Wheeler
-License: BSD-Easel
-
-Files: easel/esl_regexp.c
-Copyright: © 1986, 1993, 1995 by University of Toronto
-License: BSD-Easel
-
-Files: easel/*
-Copyright: © 2004-2008 Sean R. Eddy
- © 2006-2008 Howard Hughes Medical Institute
-License: BSD-Easel
-
-License: BSD-Easel
- @EASEL_COPYRIGHT@
- .
- The Easel library is freely modifiable and redistributable under the
- Janelia Farm Software License, a BSD license:
- .
- 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. Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in
- the documentation and/or other materials provided with the
- distribution.
- .
- 3. Neither the name of the Howard Hughes Medical Institute nor the
- names of its contributors may be used to endorse or promote
- products derived from this software without specific prior written
- permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY,
- NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE ARE
- DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
- LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
- REASONABLE ROYALTIES; 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: Userguide.pdf
-Copyright: Sean R. Eddy
-License: GPL-3
-Comment: The PDFs that are coming with the sources from which the userguide is
- built are indeed upstream's original sources. They are edited with a PDF
- editor. Upstream, Dr Eddy, was consulted in this issue.
-
-
-Files: *
-Copyright: © 2001-2013 HHMI Janelia Farm
- © 1991-2013 Sean R. Eddy
- © 2005-2013 Eric P. Nawrocki
- © 2005-2011 Diana L. Kolbe
- © 2004 Zasha Weinberg
- © 1990 Don G. Gilbert
- © 1995-2006 Washington University in St. Louis
- © 1992-1995 Medical Research Council, UK
- © 2004 University of Washington, Seattle
- © 1986,1993,1995 University of Toronto
- © 1989-2001 Free Software Foundation
- © 1991 Massachusetts Institute of Technology
-License: GPL-3
-
-License: GPL-3
- This suite of programs 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.
- .
- In other words, you may modify, copy, or redistribute this source code
- and its documentation, but if you do, you must preserve all these
- copyrights and distribute all derivative versions as free software
- under the GNU General Public License.
- .
- 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. See the GNU
- General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this software, in the file LICENSE; if not, write to the
- Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston,
- MA 02110-1301, USA or see http://www.gnu.org/
-Comment: On Debian systems, the complete text of the GNU General Public
- License version 3 can be found in `/usr/share/common-licenses/GPL-3'.
Copied: trunk/packages/infernal/tags/1.1.1-1/debian/copyright (from rev 17646, trunk/packages/infernal/trunk/debian/copyright)
===================================================================
--- trunk/packages/infernal/tags/1.1.1-1/debian/copyright (rev 0)
+++ trunk/packages/infernal/tags/1.1.1-1/debian/copyright 2014-08-08 13:16:56 UTC (rev 17657)
@@ -0,0 +1,143 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Infernal developer team at HHMI Janelia Farm:
+ Diana Kolbe <kolbed janelia.hhmi.org>
+ Eric Nawrocki <nawrockie janelia.hhmi.org>
+ Sean Eddy <eddys janelia.hhmi.org>.
+Source: ftp://infernal.janelia.org/pub/software/infernal/infernal-1.1.1.tar.gz
+
+Files: debian/*
+Copyright: © 2007-2008 Steffen Moeller <moeller at debian.org>
+ © 2009-2013 Andreas Tille <tille at debian.org>
+License: GPL-3
+
+Files: rigfilters/*
+Copyright: © 2004, Zasha Weinberg
+License: BSD-like
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ .
+ - Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ - Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+ - Neither the name of the University of Washington nor the names of
+ its contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+ NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
+ SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
+ IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Files: easel/esl_sse.c easel/esl_vmx.c
+Copyright: © 2007 Julien Pommier
+ © 1992 Stephen Moshier
+License: BSD-Easel
+
+Files: easel/easel.c::esl_tmpfile()
+Copyright: © 1999-2001 David A. Wheeler
+License: BSD-Easel
+
+Files: easel/esl_regexp.c
+Copyright: © 1986, 1993, 1995 by University of Toronto
+License: BSD-Easel
+
+Files: easel/*
+Copyright: © 2004-2008 Sean R. Eddy
+ © 2006-2008 Howard Hughes Medical Institute
+License: BSD-Easel
+
+License: BSD-Easel
+ @EASEL_COPYRIGHT@
+ .
+ The Easel library is freely modifiable and redistributable under the
+ Janelia Farm Software License, a BSD license:
+ .
+ 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. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in
+ the documentation and/or other materials provided with the
+ distribution.
+ .
+ 3. Neither the name of the Howard Hughes Medical Institute nor the
+ names of its contributors may be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY,
+ NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+ REASONABLE ROYALTIES; 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: Userguide.pdf
+Copyright: Sean R. Eddy
+License: GPL-3
+Comment: The PDFs that are coming with the sources from which the userguide is
+ built are indeed upstream's original sources. They are edited with a PDF
+ editor. Upstream, Dr Eddy, was consulted in this issue.
+
+
+Files: *
+Copyright: © 2001-2014 HHMI Janelia Farm
+ © 1991-2013 Sean R. Eddy
+ © 2005-2013 Eric P. Nawrocki
+ © 2005-2011 Diana L. Kolbe
+ © 2004 Zasha Weinberg
+ © 1990 Don G. Gilbert
+ © 1995-2006 Washington University in St. Louis
+ © 1992-1995 Medical Research Council, UK
+ © 2004 University of Washington, Seattle
+ © 1986,1993,1995 University of Toronto
+ © 1989-2001 Free Software Foundation
+ © 1991 Massachusetts Institute of Technology
+License: GPL-3
+
+License: GPL-3
+ This suite of programs 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.
+ .
+ In other words, you may modify, copy, or redistribute this source code
+ and its documentation, but if you do, you must preserve all these
+ copyrights and distribute all derivative versions as free software
+ under the GNU General Public License.
+ .
+ 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. See the GNU
+ General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this software, in the file LICENSE; if not, write to the
+ Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston,
+ MA 02110-1301, USA or see http://www.gnu.org/
+Comment: On Debian systems, the complete text of the GNU General Public
+ License version 3 can be found in `/usr/share/common-licenses/GPL-3'.
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