[Collab-qa-commits] r2256 - in packages-metadata: a g i l m v

Charles Plessy plessy at alioth.debian.org
Sat May 5 03:00:39 UTC 2012 

Author: plessy
Date: 2012-05-05 03:00:39 +0000 (Sat, 05 May 2012)
New Revision: 2256

Added:
   packages-metadata/m/mrbayes.upstream
Modified:
   packages-metadata/a/adun.app.upstream
   packages-metadata/g/gromacs.upstream
   packages-metadata/i/imagevis3d.copyright
   packages-metadata/l/loki.copyright
   packages-metadata/v/vxl.copyright
Log:
Daily automatic umegaya push

Modified: packages-metadata/a/adun.app.upstream
===================================================================
--- packages-metadata/a/adun.app.upstream	2012-05-04 03:00:30 UTC (rev 2255)
+++ packages-metadata/a/adun.app.upstream	2012-05-05 03:00:39 UTC (rev 2256)
@@ -1,10 +1,8 @@
 Archive: Gna
-Reference-DOI: 10.1002/jcc.20312
 Homepage: http://diana.imim.es/Adun
 Name: Adun
-Reference-PMID: 16175583
 Reference:
- Author: Michael A. Johnston, Ignacio Fdez. Galván and Jordi Villà-Freixa
+ Author: Michael A. Johnston and Ignacio Fdez. Galván and Jordi Villà-Freixa
  Title: >
   Framework-based design of a new all-purpose molecular simulation application: The Adun simulator
  Journal: J. Comp. Chem.
@@ -12,6 +10,8 @@
  Number: 15
  Pages: 1647-1659
  Year: 2005
+ DOI: 10.1002/jcc.20312
+ PMID: 16175583
  URL: http://www3.interscience.wiley.com/journal/112094040/abstract
 Screenshots: http://cbbl.imim.es:8080/Adun/screenshots
 Watch: |

Modified: packages-metadata/g/gromacs.upstream
===================================================================
--- packages-metadata/g/gromacs.upstream	2012-05-04 03:00:30 UTC (rev 2255)
+++ packages-metadata/g/gromacs.upstream	2012-05-05 03:00:39 UTC (rev 2256)
@@ -1,6 +1,6 @@
 Name: GROMACS
 Reference:
- - Author: B. Hess, C. Kutzner, D. van der Spoel, E. Lindahl
+ - Author: Hess, Berk and Kutzner, Carsten and van der Spoel, David and Lindahl, Erik
    Title: "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation"
    Journal: J. Chem. Theory Comput.
    Year: 2008
@@ -8,14 +8,18 @@
    Number: 3
    Pages: 435-447
    URL: http://pubs.acs.org/doi/abs/10.1021/ct700301q
+   eprint: http://pubs.acs.org/doi/pdfplus/10.1021/ct700301q
    DOI: 10.1021/ct700301q
- - Author: Lindahl E, Hess B, van der Spoel D.
+ - Author: Lindahl, Erik and Hess, Berk and van der Spoel, David
    Title: "GROMACS 3.0: A Package for Molecular Simulation and Trajectory Analysis"
    Journal: J Mol Model.
    Year: 2001
    Volume: 7
    Number: 8
    Pages: 306-17
+   DOI: 10.1007/s008940100045
+   URL: http://www.springerlink.com/content/r894b1jx35la6eja/
+   eprint: http://www.springerlink.com/content/r894b1jx35la6eja/fulltext.pdf
  - Author: Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ
    Title: "GROMACS: Fast, Flexible, and Free"
    Journal: J Comput Chem.
@@ -24,3 +28,6 @@
    Number: 16
    Pages: 1701-18
    PMID: 16211538
+   DOI: 10.1002/jcc.20291
+   URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20291/abstract
+   eprint: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20291/pdf

Modified: packages-metadata/i/imagevis3d.copyright
===================================================================
--- packages-metadata/i/imagevis3d.copyright	2012-05-04 03:00:30 UTC (rev 2255)
+++ packages-metadata/i/imagevis3d.copyright	2012-05-05 03:00:39 UTC (rev 2256)
@@ -1,4 +1,4 @@
-Format: http://dep.debian.net/deps/dep5/
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: ImageVis3D
 Upstream-Contact: Tom Fogal
 Source: http://www.imagevis3d.com
@@ -30,6 +30,6 @@
  DEALINGS IN THE SOFTWARE.
 
 Files: debian/*
-Copyright: 2011; Mathieu Malaterre <mathieu.malaterre at gmail.com>
+Copyright: 2011; Mathieu Malaterre <malat at debian.org>
 License: MIT
  Same as above

Modified: packages-metadata/l/loki.copyright
===================================================================
--- packages-metadata/l/loki.copyright	2012-05-04 03:00:30 UTC (rev 2255)
+++ packages-metadata/l/loki.copyright	2012-05-05 03:00:39 UTC (rev 2256)
@@ -1,35 +1,41 @@
-This package was debianized by Carleos Artime <carleos at uniovi.es> 
-on 2004-09-24.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Loki
+Upstream-Contact: Simon C. Heath <heath at cng.fr>
+Source: http://web.archive.org/web/20051220050931/http://loki.homeunix.net/
+        (web archive because original page vanished)
 
-It was downloaded from http://loki.homeunix.net.
+Files: *
+Copyright: 1997-2004 Simon C. Heath <heath at cng.fr>
+License: BSD
 
-Upstream Author: Simon C. Heath <heath at cng.fr>
+Files: debian/*
+Copyright: 2003-2004 Carleos Artime <carleos at uniovi.es>
+           2008-2012 Andreas Tille <tille at debian.org>
+License: BSD
 
-Copyright: (c) 1997-2004 by Simon C. Heath.
+License: BSD
+ Loki source is available under a modified version of the BSD license:
+ .
+ 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.
+ 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.
 
-License:
-
-Loki source is available under a modified version of the BSD license:
-
-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.
-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.

Added: packages-metadata/m/mrbayes.upstream
===================================================================
--- packages-metadata/m/mrbayes.upstream	                        (rev 0)
+++ packages-metadata/m/mrbayes.upstream	2012-05-05 03:00:39 UTC (rev 2256)
@@ -0,0 +1,31 @@
+Reference:
+ - Author: Fredrik Ronquist and Maxim Teslenko and Paul van der Mark and Daniel L. Ayres and Aaron Darling and Sebastian Höhna and Bret Larget and Liang Liu and Marc A. Suchard and John P. Huelsenbeck
+   Title: "MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space"
+   Journal: Systematic Biology
+   Year: 2012
+   DOI: 10.1093/sysbio/sys029
+   PMID: 22357727
+   URL: http://sysbio.oxfordjournals.org/content/early/2012/03/02/sysbio.sys029.abstract
+   eprint: http://sysbio.oxfordjournals.org/content/early/2012/03/02/sysbio.sys029.full.pdf+html
+ - Author: Fredrik Ronquist and John P. Huelsenbeck
+   Title: "MrBayes 3: Bayesian phylogenetic inference under mixed models"
+   Journal: Bioinformatics
+   Year: 2003
+   Volume: 19
+   Number: 12
+   Pages: 1572-1574
+   DOI: 10.1093/bioinformatics/btg180
+   PMID: 12912839
+   URL: http://bioinformatics.oxfordjournals.org/content/19/12/1572.abstract
+   eprint: http://bioinformatics.oxfordjournals.org/content/19/12/1572.full.pdf+html
+ - Author: John P. Huelsenbeck and Fredrik Ronquist
+   Title: "MRBAYES: Bayesian inference of phylogenetic trees"
+   Journal: Bioinformatics
+   Year: 2001
+   Volume: 17
+   Number: 8
+   Pages: 754-755
+   DOI: 10.1093/bioinformatics/17.8.754
+   PMID: 11524383
+   URL: http://bioinformatics.oxfordjournals.org/content/17/8/754.abstract
+   eprint: http://bioinformatics.oxfordjournals.org/content/17/8/754.full.pdf+html

Modified: packages-metadata/v/vxl.copyright
===================================================================
--- packages-metadata/v/vxl.copyright	2012-05-04 03:00:30 UTC (rev 2255)
+++ packages-metadata/v/vxl.copyright	2012-05-05 03:00:39 UTC (rev 2256)
@@ -1,9 +1,7 @@
-Format-Specification: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Debianized-By: Mathieu Malaterre <mathieu.malaterre at gmail.com>
-Debianized-Date: Wed, 30 Sep 2009 14:07:28 +0200
-Original-Source: http://vxl.sourceforge.net
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: VXL
+Source: http://vxl.sourceforge.net
 
-
 Files: *
 Copyright:
           Copyright (c) 2000-2003 TargetJr Consortium
@@ -88,8 +86,8 @@
  .
  You should have received a copy of the GNU General Public License
  along with VRweb; see the file LICENCE. If not, write to the
- Free Software Foundation, Inc., 59 Temple Place - Suite 330,
- Boston, MA 02111-1307, USA.
+ Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA 02110-1301, USA.
 
 Files: v3p/zlib/*
 Copyright:

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