gmane.linux.debian.devel.medical.scm

r11014 - trunk/packages/kempbasu/trunk/debian

Andreas Tille — 2012-05-26T05:40:09

Author: tille
Date: 2012-05-26 05:40:08 +0000 (Sat, 26 May 2012)
New Revision: 11014

Modified:
   trunk/packages/kempbasu/trunk/debian/copyright
Log:
DEP5 skeleton


Modified: trunk/packages/kempbasu/trunk/debian/copyright
===================================================================
--- trunk/packages/kempbasu/trunk/debian/copyright2012-05-25 17:33:45 UTC (rev 11013)
+++ trunk/packages/kempbasu/trunk/debian/copyright2012-05-26 05:40:08 UTC (rev 11014)
< at >< at > -1,24 +1,10 < at >< at >
-This package was debianized by Charles Plessy <plessy< at >debian.org> on
-Tue, 27 Jan 2009 18:59:06 +0900.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: http://code.google.com/p/kempbasu/downloads/list
 
-It was downloaded from <url://example.com>
+Files: *
+Copyright: © 2007-2008 <upstream>
+License: GPL-3
 
-Upstream Author(s):
-
-    <put author's name and email here>
-    <likewise for another author>
-
-Copyright:
-
-    <Copyright (C) YYYY Name OfAuthor>
-    <likewise for another author>
-
-

r11013 - trunk/packages/haploview/trunk/debian

Andreas Tille — 2012-05-25T17:33:45

Author: tille
Date: 2012-05-25 17:33:45 +0000 (Fri, 25 May 2012)
New Revision: 11013

Modified:
   trunk/packages/haploview/trunk/debian/changelog
   trunk/packages/haploview/trunk/debian/control
   trunk/packages/haploview/trunk/debian/copyright
Log:
Fixing machine readable information


Modified: trunk/packages/haploview/trunk/debian/changelog
===================================================================
--- trunk/packages/haploview/trunk/debian/changelog2012-05-25 17:27:06 UTC (rev 11012)
+++ trunk/packages/haploview/trunk/debian/changelog2012-05-25 17:33:45 UTC (rev 11013)
< at >< at > -1,4 +1,4 < at >< at >
-haploview (4.0-1) UNRELEASED; urgency=low
+haploview (4.1-1) UNRELEASED; urgency=low
 
   * Initial release (Closes: #311421)
 

Modified: trunk/packages/haploview/trunk/debian/control
===================================================================
--- trunk/packages/haploview/trunk/debian/control2012-05-25 17:27:06 UTC (rev 11012)
+++ trunk/packages/haploview/trunk/debian/control2012-05-25 17:33:45 UTC (

r11012 - in trunk: . package_template

Andreas Tille — 2012-05-25T17:27:07

Author: tille
Date: 2012-05-25 17:27:06 +0000 (Fri, 25 May 2012)
New Revision: 11012

Added:
   trunk/package_template/
   trunk/package_template/changelog
   trunk/package_template/compat
   trunk/package_template/control
   trunk/package_template/copyright
   trunk/package_template/rules
   trunk/package_template/upstream
Log:
Very simple template for machine-readable files to simplify creating new packages which are typical for Debian Med team


Added: trunk/package_template/changelog
===================================================================
--- trunk/package_template/changelog                        (rev 0)
+++ trunk/package_template/changelog2012-05-25 17:27:06 UTC (rev 11012)
< at >< at > -0,0 +1,5 < at >< at >
+<pkg> (<version>-1) unstable; urgency=low
+
+  * Initial release (Closes: #<bug>)
+
+ -- DMPT <debian-med-packaging< at >lists.alioth.debian.org> <date>

Added: trunk/package_template/compat
===================================================================
--- trunk/package_template/compat

r11011 - trunk/packages/haploview

Andreas Tille — 2012-05-25T17:19:46

Author: tille
Date: 2012-05-25 17:19:46 +0000 (Fri, 25 May 2012)
New Revision: 11011

Removed:
   trunk/packages/haploview/branches/
Log:
There is no point in keeping upstream stuff in SVN

r11010 - trunk/packages/grogui/trunk/debian

Andreas Tille — 2012-05-25T13:19:37

Author: tille
Date: 2012-05-25 13:19:36 +0000 (Fri, 25 May 2012)
New Revision: 11010

Modified:
   trunk/packages/grogui/trunk/debian/control
Log:
Take over better description from task file


Modified: trunk/packages/grogui/trunk/debian/control
===================================================================
--- trunk/packages/grogui/trunk/debian/control2012-05-25 13:17:41 UTC (rev 11009)
+++ trunk/packages/grogui/trunk/debian/control2012-05-25 13:19:36 UTC (rev 11010)
< at >< at > -9,6 +9,15 < at >< at >
 Package: grogui
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: <insert up to 60 chars description>
+Description: graphical user interface for popular molecular dynamics package GROMACS
  Gromacs GUI is a Qt4-based graphical user interface for widely used molecular
  dynamics package, GROMACS.
+ .
+  1. File browsing and management with customizable right-click pop up menu.
+  2. Graphical interfaces for GROMACS commands (currently 21 commands have their own interfaces).
+  3. Plot drawing

r11009 - trunk/packages/grogui/trunk/debian

Andreas Tille — 2012-05-25T13:17:42

Author: tille
Date: 2012-05-25 13:17:41 +0000 (Fri, 25 May 2012)
New Revision: 11009

Modified:
   trunk/packages/grogui/trunk/debian/copyright
Log:
DEP5


Modified: trunk/packages/grogui/trunk/debian/copyright
===================================================================
--- trunk/packages/grogui/trunk/debian/copyright2012-05-25 12:49:42 UTC (rev 11008)
+++ trunk/packages/grogui/trunk/debian/copyright2012-05-25 13:17:41 UTC (rev 11009)
< at >< at > -1,40 +1,30 < at >< at >
-This package was debianized by:
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Gromacs GUI
+Source: http://kde-apps.org/content/show.php/Gromacs+GUI+?content=47665
 
-    Steffen Moeller <moeller< at >debian.org> on Sun, 23 Nov 2008 23:38:26 +0100
+Files: *
+Copyright: © 2008 Reza Salari <resal81< at >yahoo.com>
+License: GPL-2+
 
-It was downloaded from:
+Files: debian/*
+Copyright: © 2008 Steffen Moeller <moeller< at >debian.org>
+License: GPL-2+
 
-    http://resal.wordpress.com/gromacs-gui/
-
-Upstream Author:
-
-

r11008 - in trunk/packages/libhmsbeagle/trunk/debian: .patches

Andreas Tille — 2012-05-25T12:49:43

Author: tille
Date: 2012-05-25 12:49:42 +0000 (Fri, 25 May 2012)
New Revision: 11008

Removed:
   trunk/packages/libhmsbeagle/trunk/debian/patches/do_not_build_unused_plugin.patch
Modified:
   trunk/packages/libhmsbeagle/trunk/debian/changelog
   trunk/packages/libhmsbeagle/trunk/debian/patches/enable_static.patch
   trunk/packages/libhmsbeagle/trunk/debian/patches/series
Log:
Restore preparation for new upstream version - waiting for answer from upstream


Modified: trunk/packages/libhmsbeagle/trunk/debian/changelog
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/changelog2012-05-25 12:48:02 UTC (rev 11007)
+++ trunk/packages/libhmsbeagle/trunk/debian/changelog2012-05-25 12:49:42 UTC (rev 11008)
< at >< at > -1,3 +1,12 < at >< at >
+libhmsbeagle (1.1-1) UNRELEASED; urgency=low
+
+  * New upstream release
+     - debian/patches/disable_cpu_sse_plugin.patch:  Seems upstream
+       has solved the problem a bit differently than in this patch
+       -> droping it

r11007 - in trunk/packages/libhmsbeagle/trunk/debian: .patches

Andreas Tille — 2012-05-25T12:48:02

Author: tille
Date: 2012-05-25 12:48:02 +0000 (Fri, 25 May 2012)
New Revision: 11007

Added:
   trunk/packages/libhmsbeagle/trunk/debian/patches/do_not_build_unused_plugin.patch
Modified:
   trunk/packages/libhmsbeagle/trunk/debian/changelog
   trunk/packages/libhmsbeagle/trunk/debian/patches/enable_static.patch
   trunk/packages/libhmsbeagle/trunk/debian/patches/series
Log:
Override unconfirmed NMU with current changes in SVN; upgrade to new version needs more communication with upstream and is thus delayed; also delayed hardening


Modified: trunk/packages/libhmsbeagle/trunk/debian/changelog
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/changelog2012-05-25 12:29:48 UTC (rev 11006)
+++ trunk/packages/libhmsbeagle/trunk/debian/changelog2012-05-25 12:48:02 UTC (rev 11007)
< at >< at > -1,9 +1,5 < at >< at >
-libhmsbeagle (1.1-1) UNRELEASED; urgency=low
+libhmsbeagle (1.0-6) unstable; urgency=low
 
-  * New upstream release
-     - debian/patches/disable_cpu_sse

r11006 - trunk/packages/libforester-java/trunk/debian

Olivier Sallou — 2012-05-25T12:29:49

Author: osallou
Date: 2012-05-25 12:29:48 +0000 (Fri, 25 May 2012)
New Revision: 11006

Modified:
   trunk/packages/libforester-java/trunk/debian/control
Log:
fix dependency name

Modified: trunk/packages/libforester-java/trunk/debian/control
===================================================================
--- trunk/packages/libforester-java/trunk/debian/control2012-05-25 12:26:45 UTC (rev 11005)
+++ trunk/packages/libforester-java/trunk/debian/control2012-05-25 12:29:48 UTC (rev 11006)
< at >< at > -23,7 +23,7 < at >< at >
 Package: libforester-java
 Architecture: all
 Depends: ${misc:Depends},
- libcommons-codec, libitext-java
+ libcommons-codec-java, libitext-java
 Description: Libraries for evolutionary biology and comparative genomics research
  Forester is a library of Java software for phylogenomics 
  and evolutionary biology research. It can be used to read or

r11005 - trunk/packages/libforester-java/trunk/debian

Olivier Sallou — 2012-05-25T12:26:46

Author: osallou
Date: 2012-05-25 12:26:45 +0000 (Fri, 25 May 2012)
New Revision: 11005

Modified:
   trunk/packages/libforester-java/trunk/debian/control
Log:
fix dependency name

Modified: trunk/packages/libforester-java/trunk/debian/control
===================================================================
--- trunk/packages/libforester-java/trunk/debian/control2012-05-25 12:12:50 UTC (rev 11004)
+++ trunk/packages/libforester-java/trunk/debian/control2012-05-25 12:26:45 UTC (rev 11005)
< at >< at > -5,7 +5,7 < at >< at >
 DM-Upload-Allowed: yes
 Uploaders: Olivier Sallou <osallou< at >debian.org>
 Build-Depends: debhelper (>= 8.0.0),
- default-jdk, junit4, javahelper (>=0.25), libcommons-codec, libitext-java
+ default-jdk, junit4, javahelper (>=0.25), libcommons-codec-java, libitext-java
 Standards-Version: 3.9.3
 Homepage: http://code.google.com/p/forester
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/forester/trunk/

r11004 - trunk/packages/fasttree/trunk/debian

Andreas Tille — 2012-05-25T12:12:50

Author: tille
Date: 2012-05-25 12:12:50 +0000 (Fri, 25 May 2012)
New Revision: 11004

Modified:
   trunk/packages/fasttree/trunk/debian/copyright
Log:
DEP5


Modified: trunk/packages/fasttree/trunk/debian/copyright
===================================================================
--- trunk/packages/fasttree/trunk/debian/copyright2012-05-25 12:07:10 UTC (rev 11003)
+++ trunk/packages/fasttree/trunk/debian/copyright2012-05-25 12:12:50 UTC (rev 11004)
< at >< at > -1,10 +1,8 < at >< at >
-Format: http://dep.debian.net/deps/dep5
-Upstream-Name: fasttree
-Source: <url://example.com>
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: FastTree
+Source: http://www.microbesonline.org/fasttree/#Install
 
 Files: *
-Copyright: <years> <put author's name and email here>
-           <years> <likewise for another author>
 Copyright: (C) 2008-2009 The Regents of the University of California
 License: GPL-2.0+
 
< at >< at > -29,13 +27,3 < at >< at >
  On Debian systems, the complete text of the GNU General
  Public Lic

r11003 - trunk/packages/ecell/trunk/debian

Andreas Tille — 2012-05-25T12:07:11

Author: tille
Date: 2012-05-25 12:07:10 +0000 (Fri, 25 May 2012)
New Revision: 11003

Modified:
   trunk/packages/ecell/trunk/debian/copyright
Log:
Pseudo-DEP5 to enable machine-readable gatherer fetch license


Modified: trunk/packages/ecell/trunk/debian/copyright
===================================================================
--- trunk/packages/ecell/trunk/debian/copyright2012-05-25 12:02:58 UTC (rev 11002)
+++ trunk/packages/ecell/trunk/debian/copyright2012-05-25 12:07:10 UTC (rev 11003)
< at >< at > -1,10 +1,11 < at >< at >
-This package was debianized by Steffen Moeller <moeller< at >unknown> on
-Wed, 10 Mar 2004 22:08:00 +0100.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: E-Cell
+Source: https://github.com/ecell/ecell.github.com
 
-It was downloaded from <fill in ftp site>
+Files: *
+Copyright: © -2003 ???
+License: GPL
 
-Upstream Author(s): <put author(s) name and email here>
-
-Copyright:
-
-<Must follow here>
+Files: debian/*
+Copyright: © 2004 Steffen Moeller <moeller< at >

r11002 - trunk/packages/ecell/trunk/debian

Andreas Tille — 2012-05-25T12:02:58

Author: tille
Date: 2012-05-25 12:02:58 +0000 (Fri, 25 May 2012)
New Revision: 11002

Modified:
   trunk/packages/ecell/trunk/debian/control
Log:
Team maintained package


Modified: trunk/packages/ecell/trunk/debian/control
===================================================================
--- trunk/packages/ecell/trunk/debian/control2012-05-25 11:48:20 UTC (rev 11001)
+++ trunk/packages/ecell/trunk/debian/control2012-05-25 12:02:58 UTC (rev 11002)
< at >< at > -1,7 +1,9 < at >< at >
 Source: ecell
 Section: science
 Priority: optional
-Maintainer: Steffen Moeller <moeller< at >pzr.uni-rostock.de>
+Maintainer: Debian Med Packaging Team <debian-med-packaging< at >lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller< at >pzr.uni-rostock.de>
 Build-Depends: debhelper (>= 4.0.0), python-numpy, python-dev, python-gtk2, python-glade2, g++ (>= 3.3), libgsl0-dev, libboost-python-dev, automake, autoconf, libtool, python-gnome2, expect, doxygen, graphviz, docbook-utils, ghostscript, docbook-to-man
 Standards-Version:

r11001 - in trunk/packages: . logomat-m logomat-m/trunklogomat-m/trunk/debian

Andreas Tille — 2012-05-25T11:48:20

Author: tille
Date: 2012-05-25 11:48:20 +0000 (Fri, 25 May 2012)
New Revision: 11001

Added:
   trunk/packages/logomat-m/
   trunk/packages/logomat-m/trunk/
   trunk/packages/logomat-m/trunk/debian/
   trunk/packages/logomat-m/trunk/debian/changelog
   trunk/packages/logomat-m/trunk/debian/compat
   trunk/packages/logomat-m/trunk/debian/control
   trunk/packages/logomat-m/trunk/debian/copyright
   trunk/packages/logomat-m/trunk/debian/upstream
Log:
Inject data from med-bio task file as machine readable packaging files to enable machine-readable gatherer fetching it


Added: trunk/packages/logomat-m/trunk/debian/changelog
===================================================================
--- trunk/packages/logomat-m/trunk/debian/changelog                        (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/changelog2012-05-25 11:48:20 UTC (rev 11001)
< at >< at > -0,0 +1,5 < at >< at >
+logomat-m (0.0.20091119-1) unstable; urgency=low
+
+  * Initial release
+
+ -- Andreas Tille <tille< at >debian.org>  Thu, 24 May 2012 14:30:1

r11000 - in trunk/packages/dcmtk/trunk/debian: . patches

Mathieu Malaterre — 2012-05-25T09:51:26

Author: malat
Date: 2012-05-25 09:51:25 +0000 (Fri, 25 May 2012)
New Revision: 11000

Added:
   trunk/packages/dcmtk/trunk/debian/patches/bug674361.patch
Modified:
   trunk/packages/dcmtk/trunk/debian/changelog
   trunk/packages/dcmtk/trunk/debian/control
   trunk/packages/dcmtk/trunk/debian/patches/series
   trunk/packages/dcmtk/trunk/debian/rules
Log:
Work on dcmtk package/gcc 4.7 issue

Modified: trunk/packages/dcmtk/trunk/debian/changelog
===================================================================
--- trunk/packages/dcmtk/trunk/debian/changelog2012-05-25 08:46:12 UTC (rev 10999)
+++ trunk/packages/dcmtk/trunk/debian/changelog2012-05-25 09:51:25 UTC (rev 11000)
< at >< at > -1,3 +1,11 < at >< at >
+dcmtk (3.6.0-11) UNRELEASED; urgency=low
+
+  * Fix compilation with gcc 4.7. Closes: #674361
+   - debian/patches/bug674361.patch
+  * Make sure to link against libxml2
+
+ -- Mathieu Malaterre <malat< at >debian.org>  Fri, 25 May 2012 11:19:22 +0200
+
 dcmtk (3.6.0-10) unstable; urgency=low
 
   [ Andreas Tille ]

Modified:

r10999 - trunk/packages/sift/trunk/debian

Andreas Tille — 2012-05-25T08:46:13

Author: tille
Date: 2012-05-25 08:46:12 +0000 (Fri, 25 May 2012)
New Revision: 10999

Added:
   trunk/packages/sift/trunk/debian/upstream
Modified:
   trunk/packages/sift/trunk/debian/changelog
Log:
Citation of the day


Modified: trunk/packages/sift/trunk/debian/changelog
===================================================================
--- trunk/packages/sift/trunk/debian/changelog2012-05-24 21:26:20 UTC (rev 10998)
+++ trunk/packages/sift/trunk/debian/changelog2012-05-25 08:46:12 UTC (rev 10999)
< at >< at > -1,3 +1,9 < at >< at >
+sift (4.0.3b-4) UNRELEASED; urgency=low
+
+  * debian/upstream: Add citations
+
+ -- Andreas Tille <tille< at >debian.org>  Fri, 25 May 2012 10:45:33 +0200
+
 sift (4.0.3b-3) unstable; urgency=low
 
   * Added patches from Michael Bienia <geser< at >ubuntu.com>.

Added: trunk/packages/sift/trunk/debian/upstream
===================================================================
--- trunk/packages/sift/trunk/debian/upstream                        (rev 0)
+++ trunk/packages/sift/trunk/debian/upstream201

r10998 - in trunk/packages: . amos amos/trunkamos/trunk/debian

Andreas Tille — 2012-05-24T21:26:20

Author: tille
Date: 2012-05-24 21:26:20 +0000 (Thu, 24 May 2012)
New Revision: 10998

Added:
   trunk/packages/amos/
   trunk/packages/amos/trunk/
   trunk/packages/amos/trunk/debian/
   trunk/packages/amos/trunk/debian/changelog
   trunk/packages/amos/trunk/debian/compat
   trunk/packages/amos/trunk/debian/control
   trunk/packages/amos/trunk/debian/copyright
   trunk/packages/amos/trunk/debian/upstream
   trunk/packages/amos/trunk/debian/watch
Log:
Add machine-readable data for amos-assembler and hawkeye which both build from the same source


Added: trunk/packages/amos/trunk/debian/changelog
===================================================================
--- trunk/packages/amos/trunk/debian/changelog                        (rev 0)
+++ trunk/packages/amos/trunk/debian/changelog2012-05-24 21:26:20 UTC (rev 10998)
< at >< at > -0,0 +1,5 < at >< at >
+amos (3.1.0-1) unstable; urgency=low
+
+  * Initial release
+
+ -- Andreas Tille <tille< at >debian.org>  Thu, 24 May 2012 14:30:13 +0200

Added: trunk/packages/amos/trunk/debian/

r10997 - trunk/packages/pdb2pqr/trunk/debian

Michael Banck — 2012-05-24T15:30:50

Author: mbanck
Date: 2012-05-24 15:30:49 +0000 (Thu, 24 May 2012)
New Revision: 10997

Modified:
   trunk/packages/pdb2pqr/trunk/debian/upstream
Log:
Add name, homepage and registration fields to upstream metadata

Modified: trunk/packages/pdb2pqr/trunk/debian/upstream
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/upstream2012-05-24 15:23:06 UTC (rev 10996)
+++ trunk/packages/pdb2pqr/trunk/debian/upstream2012-05-24 15:30:49 UTC (rev 10997)
< at >< at > -1,3 +1,6 < at >< at >
+Name: PDB2PQR
+Homepage: http://www.poissonboltzmann.org/pdb2pqr
+Registration: http://spreadsheets.google.com/viewform?hl=en&formkey=dHFpa3Nvcnl0cjR1U3g3UTdSYU1pWWc6MA..
 Reference:
  - Author: Todd J Dolinsky and Paul Czodrowski and Hui Li and Jens E Nielsen and Jan H Jensen and Gerhard Klebe and Nathan A Baker
    Title: "PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations"

r10996 - in trunk/packages/libforester-java/trunk: .debian debian/binary debian/patches debian/source

Olivier Sallou — 2012-05-24T15:23:06

Author: osallou
Date: 2012-05-24 15:23:06 +0000 (Thu, 24 May 2012)
New Revision: 10996

Added:
   trunk/packages/libforester-java/trunk/debian/
   trunk/packages/libforester-java/trunk/debian/binary/
   trunk/packages/libforester-java/trunk/debian/binary/forester
   trunk/packages/libforester-java/trunk/debian/changelog
   trunk/packages/libforester-java/trunk/debian/compat
   trunk/packages/libforester-java/trunk/debian/control
   trunk/packages/libforester-java/trunk/debian/copyright
   trunk/packages/libforester-java/trunk/debian/docs
   trunk/packages/libforester-java/trunk/debian/forester.install
   trunk/packages/libforester-java/trunk/debian/get-orig-source.sh
   trunk/packages/libforester-java/trunk/debian/libforester-java-doc.doc-base
   trunk/packages/libforester-java/trunk/debian/libforester-java-doc.install
   trunk/packages/libforester-java/trunk/debian/libforester-java.jlibs
   trunk/packages/libforester-java/trunk/debian/patches/
   trunk/packages/libforester-java/trunk/debian/patches/change_i

r10995 - trunk/packages/libforester-java

Olivier Sallou — 2012-05-24T15:23:02

Author: osallou
Date: 2012-05-24 15:23:01 +0000 (Thu, 24 May 2012)
New Revision: 10995

Added:
   trunk/packages/libforester-java/trunk/
Log:
Creating trunk directory

r10994 - in trunk/packages: . libforester-java

Olivier Sallou — 2012-05-24T15:22:57

Author: osallou
Date: 2012-05-24 15:22:57 +0000 (Thu, 24 May 2012)
New Revision: 10994

Added:
   trunk/packages/libforester-java/
   trunk/packages/libforester-java/tags/
Log:
[svn-inject] Creating libforester-java/tags/ directory.