[med-svn] r7819 - in trunk/packages/seqan/tags: . 1.3-1/debian
Charles Plessy
plessy at alioth.debian.org
Fri Sep 16 04:18:57 UTC 2011
Author: plessy
Date: 2011-09-16 04:18:57 +0000 (Fri, 16 Sep 2011)
New Revision: 7819
Added:
trunk/packages/seqan/tags/1.3-1/
trunk/packages/seqan/tags/1.3-1/debian/changelog
trunk/packages/seqan/tags/1.3-1/debian/control
trunk/packages/seqan/tags/1.3-1/debian/copyright
Removed:
trunk/packages/seqan/tags/1.3-1/debian/changelog
trunk/packages/seqan/tags/1.3-1/debian/control
trunk/packages/seqan/tags/1.3-1/debian/copyright
Log:
[svn-buildpackage] Tagging seqan 1.3-1
Deleted: trunk/packages/seqan/tags/1.3-1/debian/changelog
===================================================================
--- trunk/packages/seqan/trunk/debian/changelog 2011-09-15 15:47:39 UTC (rev 7815)
+++ trunk/packages/seqan/tags/1.3-1/debian/changelog 2011-09-16 04:18:57 UTC (rev 7819)
@@ -1,26 +0,0 @@
-seqan (1.3-1) UNRELEASED; urgency=low
-
- * New upstream release (Closes: #640302).
-
- [ Charles Plessy ]
- * Collected various informations in ‘debian/upstream-metadata.yaml’.
- * Compress the source and binary packages with xz
- (debian/orig-tar.sh, debian/rules).
- * Use Debhelper 8 (debian/compat, debian/control).
- * Conforms to Policy 3.9.2 (debian/control, no other changes needed).
-
- [ Andreas Tille ]
- * debian/control
- - added myself to uploaders
- - Standards-Version: 3.9.1 (no changes needed)
- - debhelper 7
- * debian/watch: Allso catch RC candidates
- * debian/source/format: 3.0 (quilt)
-
- -- Andreas Tille <tille at debian.org> Mon, 24 Jan 2011 15:38:44 +0100
-
-seqan (1.2-1) unstable; urgency=low
-
- * Initial Release (Closes: #487361)
-
- -- Soeren Sonnenburg <sonne at debian.org> Wed, 30 Sep 2009 20:41:39 +0200
Copied: trunk/packages/seqan/tags/1.3-1/debian/changelog (from rev 7818, trunk/packages/seqan/trunk/debian/changelog)
===================================================================
--- trunk/packages/seqan/tags/1.3-1/debian/changelog (rev 0)
+++ trunk/packages/seqan/tags/1.3-1/debian/changelog 2011-09-16 04:18:57 UTC (rev 7819)
@@ -0,0 +1,37 @@
+seqan (1.3-1) unstable; urgency=low
+
+ * Team upload.
+ * New upstream release (Closes: #640302).
+
+ [ Charles Plessy ]
+ * Collected various informations in ‘debian/upstream-metadata.yaml’.
+ * Compress the source and binary packages with xz
+ (debian/orig-tar.sh, debian/rules).
+ * Removed convenience code copy of samtools (debian/orig-tar.sh).
+ * Use Debhelper 8 (debian/compat, debian/control).
+ * Conforms to Policy 3.9.2 (debian/control, no other changes needed).
+ * Built using the cmake class of CDBS (debian/rules).
+ * debian/control:
+ - Corrected VCS URLs.
+ - Build-Depend on libboost-dev as Cmake was looking for it.
+ - Build-Depend on zlib1g-dev, as seqan needs to detect zlib to set
+ SEQAN_HAS_SAMTOOLS to 1.
+ - Changed Priority from extra to optional.
+ - Changed sequan-apps Section from libdevel to science.
+ * debian/patch/samtools.patch corrects path to SAMtools headers.
+ * Machine-readable debian/copyright.
+
+ [ Andreas Tille ]
+ * debian/control
+ - added myself to uploaders
+ - Standards-Version: 3.9.1 (no changes needed)
+ * debian/watch: Allso catch RC candidates
+ * debian/source/format: 3.0 (quilt)
+
+ -- Charles Plessy <plessy at debian.org> Fri, 16 Sep 2011 12:51:39 +0900
+
+seqan (1.2-1) unstable; urgency=low
+
+ * Initial Release (Closes: #487361)
+
+ -- Soeren Sonnenburg <sonne at debian.org> Wed, 30 Sep 2009 20:41:39 +0200
Deleted: trunk/packages/seqan/tags/1.3-1/debian/control
===================================================================
--- trunk/packages/seqan/trunk/debian/control 2011-09-15 15:47:39 UTC (rev 7815)
+++ trunk/packages/seqan/tags/1.3-1/debian/control 2011-09-16 04:18:57 UTC (rev 7819)
@@ -1,39 +0,0 @@
-Source: seqan
-Section: science
-Priority: extra
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Soeren Sonnenburg <sonne at debian.org>,
- Andreas Tille <tille at debian.org>
-Build-Depends: cdbs, debhelper (>= 8), cmake, zlib1g-dev, libbam-dev, libboost-dev
-Standards-Version: 3.9.2
-Homepage: http://www.seqan.de/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/seqan/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/seqan/trunk/
-
-Package: seqan-apps
-Section: libdevel
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: C++ library for the analysis of biological sequences
- SeqAn is a C++ template library of efficient algorithms and data
- structures for the analysis of sequences with the focus on
- biological data. This library applies a unique generic design that
- guarantees high performance, generality, extensibility, and
- integration with other libraries. SeqAn is easy to use and
- simplifies the development of new software tools with a minimal loss
- of performance. This package contains the applications dfi, pair_align,
- micro_razers, seqan_tcoffee, seqcons, razers and tree_recon.
-
-Package: seqan-dev
-Section: libdevel
-Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: C++ library for the analysis of biological sequences
- SeqAn is a C++ template library of efficient algorithms and data
- structures for the analysis of sequences with the focus on
- biological data. This library applies a unique generic design that
- guarantees high performance, generality, extensibility, and
- integration with other libraries. SeqAn is easy to use and
- simplifies the development of new software tools with a minimal loss
- of performance. This package contains the developer files, documentation
- and examples.
Copied: trunk/packages/seqan/tags/1.3-1/debian/control (from rev 7817, trunk/packages/seqan/trunk/debian/control)
===================================================================
--- trunk/packages/seqan/tags/1.3-1/debian/control (rev 0)
+++ trunk/packages/seqan/tags/1.3-1/debian/control 2011-09-16 04:18:57 UTC (rev 7819)
@@ -0,0 +1,38 @@
+Source: seqan
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Soeren Sonnenburg <sonne at debian.org>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: cdbs, debhelper (>= 8), cmake, zlib1g-dev, libbam-dev, libboost-dev
+Standards-Version: 3.9.2
+Homepage: http://www.seqan.de/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/seqan/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/seqan/trunk/
+
+Package: seqan-apps
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: C++ library for the analysis of biological sequences
+ SeqAn is a C++ template library of efficient algorithms and data
+ structures for the analysis of sequences with the focus on
+ biological data. This library applies a unique generic design that
+ guarantees high performance, generality, extensibility, and
+ integration with other libraries. SeqAn is easy to use and
+ simplifies the development of new software tools with a minimal loss
+ of performance. This package contains the applications dfi, pair_align,
+ micro_razers, seqan_tcoffee, seqcons, razers and tree_recon.
+
+Package: seqan-dev
+Section: libdevel
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: C++ library for the analysis of biological sequences
+ SeqAn is a C++ template library of efficient algorithms and data
+ structures for the analysis of sequences with the focus on
+ biological data. This library applies a unique generic design that
+ guarantees high performance, generality, extensibility, and
+ integration with other libraries. SeqAn is easy to use and
+ simplifies the development of new software tools with a minimal loss
+ of performance. This package contains the developer files, documentation
+ and examples.
Deleted: trunk/packages/seqan/tags/1.3-1/debian/copyright
===================================================================
--- trunk/packages/seqan/trunk/debian/copyright 2011-09-15 15:47:39 UTC (rev 7815)
+++ trunk/packages/seqan/tags/1.3-1/debian/copyright 2011-09-16 04:18:57 UTC (rev 7819)
@@ -1,115 +0,0 @@
-Format: http://dep.debian.net/deps/dep5/
-Source: http://www.seqan.de/uploads/media/Seqan_Release_1.3.zip
-
-Files: *
-Copyright: © 2007-2010
- Andreas Döring <doering at inf.fu-berlin.de>
- David Weese <weese at inf.fu-berlin.de>
- Tobias Rausch <rausch at inf.fu-berlin.de>
- Stephan Aiche <aiche at inf.fu-berlin.de>
- Anne-Katrin Emde <emde at inf.fu-berlin.de>
- Carsten Kemena <kemena at inf.fu-berlin.de>
- Konrad Ludwig Moritz Rudolph <krudolph at inf.fu-berlin.de>
- Marcel H. Schulz. <marcel.schulz at molgen.mpg.de>
-License: LGPL-3+
-
-Files: apps/mason/* apps/rabema/* demos/tutorial/read_mapping/minimapper.cpp
-Copyright: © 2010 Manuel Holtgrewe, FU Berlin
-License: GPL-3+
-
-Files: apps/stellar/*
-Copyright: © 2010 Birte Kehr
-License: LGPL-3+
-
-Files: cmake/CMake/cuda/FindCUDA/*
-Copyright: © 2008 - 2009 NVIDIA Corporation. All rights reserved.
- © 2007-2009 Scientific Computing and Imaging Institute, University of Utah
-License: MIT-cuda
- License for the specific language governing rights and limitations under
- 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.
-Comment: bogus first line ?
-
-Files: seqan-1.3/doc/shape_predefined.h
-Copyright: © 2006-2010, Knut Reinert, FU Berlin
-License: 3BSD-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 Knut Reinert or the FU Berlin 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 KNUT REINERT OR THE FU BERLIN 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: seqan/index/index_sa_lss.h
-Copyright: © 1999, N. Jesper Larsson <jesper at cs.lth.se>
- © 2007 David Weese.
-License: other
- This software may be used freely for any purpose. However, when distributed,
- the original source must be clearly stated, and, when the source code is
- distributed, the copyright notice must be retained and any alterations in
- the code must be clearly marked. No warranty is given regarding the quality
- of this software.
-
-License: LGPL-3+
- This library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 3 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
- Lesser General Public License for more details.
-Comment:
- On Debian systems, you can find the LGPL license version 3 in
- ‘/usr/share/common-licenses/LGPL-3’.
-
-License: GPL-3+
- This program 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 3 of the License, or (at your option)
- any later version.
- .
- This program 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 <http://www.gnu.org/licenses/>.
-Comment:
- On Debian systems, you can find the GPL license version 3 in
- ‘/usr/share/common-licenses/GPL-3’.
-
Copied: trunk/packages/seqan/tags/1.3-1/debian/copyright (from rev 7816, trunk/packages/seqan/trunk/debian/copyright)
===================================================================
--- trunk/packages/seqan/tags/1.3-1/debian/copyright (rev 0)
+++ trunk/packages/seqan/tags/1.3-1/debian/copyright 2011-09-16 04:18:57 UTC (rev 7819)
@@ -0,0 +1,115 @@
+Format: http://dep.debian.net/deps/dep5/
+Source: http://www.seqan.de/uploads/media/Seqan_Release_1.3.zip
+
+Files: *
+Copyright: © 2007-2010
+ Andreas Döring <doering at inf.fu-berlin.de>
+ David Weese <weese at inf.fu-berlin.de>
+ Tobias Rausch <rausch at inf.fu-berlin.de>
+ Stephan Aiche <aiche at inf.fu-berlin.de>
+ Anne-Katrin Emde <emde at inf.fu-berlin.de>
+ Carsten Kemena <kemena at inf.fu-berlin.de>
+ Konrad Ludwig Moritz Rudolph <krudolph at inf.fu-berlin.de>
+ Marcel H. Schulz. <marcel.schulz at molgen.mpg.de>
+License: LGPL-3+
+
+Files: apps/mason/* apps/rabema/* demos/tutorial/read_mapping/minimapper.cpp
+Copyright: © 2010 Manuel Holtgrewe, FU Berlin
+License: GPL-3+
+
+Files: apps/stellar/*
+Copyright: © 2010 Birte Kehr
+License: LGPL-3+
+
+Files: cmake/CMake/cuda/FindCUDA/*
+Copyright: © 2008 - 2009 NVIDIA Corporation. All rights reserved.
+ © 2007-2009 Scientific Computing and Imaging Institute, University of Utah
+License: MIT-cuda
+ License for the specific language governing rights and limitations under
+ 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.
+Comment: bogus first line ?
+
+Files: seqan/* doc/shape_predefined.h
+Copyright: © 2006-2010, Knut Reinert, FU Berlin
+License: 3BSD-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 Knut Reinert or the FU Berlin 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 KNUT REINERT OR THE FU BERLIN 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: seqan/index/index_sa_lss.h
+Copyright: © 1999, N. Jesper Larsson <jesper at cs.lth.se>
+ © 2007 David Weese.
+License: other
+ This software may be used freely for any purpose. However, when distributed,
+ the original source must be clearly stated, and, when the source code is
+ distributed, the copyright notice must be retained and any alterations in
+ the code must be clearly marked. No warranty is given regarding the quality
+ of this software.
+
+License: GPL-3+
+ This program 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 3 of the License, or (at your option)
+ any later version.
+ .
+ This program 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 <http://www.gnu.org/licenses/>.
+Comment:
+ On Debian systems, you can find the GPL license version 3 in
+ ‘/usr/share/common-licenses/GPL-3’.
+
+License: LGPL-3+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 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
+ Lesser General Public License for more details.
+Comment:
+ On Debian systems, you can find the LGPL license version 3 in
+ ‘/usr/share/common-licenses/LGPL-3’.
+
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