[med-svn] r13845 - in trunk/packages: . profit profit/trunk profit/trunk/debian profit/trunk/debian/patches profit/trunk/debian/source

Wed Jun 5 16:19:05 UTC 2013

Author: moeller
Date: 2013-06-05 16:19:05 +0000 (Wed, 05 Jun 2013)
New Revision: 13845

Added:
   trunk/packages/profit/
   trunk/packages/profit/trunk/
   trunk/packages/profit/trunk/debian/
   trunk/packages/profit/trunk/debian/README.Debian
   trunk/packages/profit/trunk/debian/README.source
   trunk/packages/profit/trunk/debian/changelog
   trunk/packages/profit/trunk/debian/compat
   trunk/packages/profit/trunk/debian/control
   trunk/packages/profit/trunk/debian/copyright
   trunk/packages/profit/trunk/debian/docs
   trunk/packages/profit/trunk/debian/patches/
   trunk/packages/profit/trunk/debian/patches/AllowReadline.patch
   trunk/packages/profit/trunk/debian/patches/AllowRedundantCleans.patch
   trunk/packages/profit/trunk/debian/patches/series
   trunk/packages/profit/trunk/debian/profit-data.dirs
   trunk/packages/profit/trunk/debian/profit-data.install
   trunk/packages/profit/trunk/debian/profit.dirs
   trunk/packages/profit/trunk/debian/profit.install
   trunk/packages/profit/trunk/debian/profit.sh
   trunk/packages/profit/trunk/debian/rules
   trunk/packages/profit/trunk/debian/source/
   trunk/packages/profit/trunk/debian/source/format
Log:
This package is nothing for Debian Med itself, it is just another
one of those that come with source code (and consequently should
be rebuildable with our distribution) but are not redistributable.

ProFit is (sadly) a common tool in structural biology to align
two proteins. If I recall correctly (and things have not changed)
then it all starts with the centers of gravity plus a three dimensional
turning along what a sequence alignment gives us.




Property changes on: trunk/packages/profit/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
   + 1

Added: trunk/packages/profit/trunk/debian/README.Debian
===================================================================

--- trunk/packages/profit/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/README.Debian	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1,9 @@
+profit for Debian
+-----------------
+
+The license of ProFit does not allow a redistribution.
+
+The documentation is not built, since it demanded too much of LaTeX to be installed,
+also for a conversion to HTML. It ships with the original source code.
+
+ -- Steffen Moeller <moeller at debian.org>  Wed, 05 Jun 2013 17:38:14 +0200

Added: trunk/packages/profit/trunk/debian/README.source
===================================================================
--- trunk/packages/profit/trunk/debian/README.source	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/README.source	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1,9 @@
+profit for Debian
+-----------------
+
+<this file describes information about the source package, see Debian policy
+manual section 4.14. You WILL either need to modify or delete this file>
+
+
+
+

Added: trunk/packages/profit/trunk/debian/changelog
===================================================================
--- trunk/packages/profit/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/changelog	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1,5 @@
+profit (3.1-1) UNRELEASED; urgency=low
+
+  * The license does not allow a redistribution.
+
+ -- Steffen Moeller <moeller at debian.org>  Wed, 05 Jun 2013 17:38:14 +0200

Added: trunk/packages/profit/trunk/debian/compat
===================================================================
--- trunk/packages/profit/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/compat	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1 @@
+8

Added: trunk/packages/profit/trunk/debian/control
===================================================================
--- trunk/packages/profit/trunk/debian/control	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/control	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1,21 @@
+Source: profit
+Section: non-free/science
+Priority: optional
+Maintainer: Steffen Moeller <steffen_moeller at gmx.de>
+Build-Depends: debhelper (>= 8.0.0), libreadline-dev
+Standards-Version: 3.9.4
+Homepage: http://www.bioinf.org.uk/software/profit/
+#Vcs-Git: git://git.debian.org/collab-maint/profit.git
+#Vcs-Browser: http://git.debian.org/?p=collab-maint/profit.git;a=summary
+
+Package: profit
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, profit-data
+Description: Protein structure alignment
+ Nothing to be redistributed.
+
+Package: profit-data
+Architecture: all
+Recommends: profit
+Description: Help and data files for Profit
+ Nothing to be redistributed.

Added: trunk/packages/profit/trunk/debian/copyright
===================================================================
--- trunk/packages/profit/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/copyright	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1,73 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: profit
+Source: <url://example.com>
+
+Files: *
+Copyright: <years> <put author's name and email here>
+           <years> <likewise for another author>
+License: <special license>
+                                ProFit
+   .
+                     Protein Least Squares Fitting
+   .
+   .
+   .
+   .
+   ProFit is copyright Dr. Andrew C.R. Martin, SciTech Software and 
+                       UCL 1992-2009
+                       Dr. Craig Porter, UCL 2008-2009
+   Modifications and enhancements were also made while working at 
+   The University of Reading under consultancy to Inpharmatica, Ltd.
+   Development of V2.6-V3.1 was funded by the BBSRC
+   .
+   This program is not in the public domain.
+   .
+   It may not be copied or made available to third parties, but may be
+   freely used by anyone who has obtained it directly from the author's
+   Web Site. Please register your name and email address on the web site
+   when you download the software.
+   .
+   The code may not be made available on other FTP sites without express
+   permission from the author.
+   .
+   The code may be modified as required, but any modifications must be
+   documented so that the person responsible can be identified. If
+   someone else breaks this code, the author doesn't want to be blamed
+   for code that does not work! You may not distribute any
+   modifications, but are encouraged to send them to the author so
+   that they may be incorporated into future versions of the code.
+   .
+   The code may not be sold commercially, but the program may be used for 
+   commercial purposes.
+   .
+   IN NO EVENT SHALL THE AUTHOR OR ANY INSTITUTION IN WHICH HE IS WORKING
+   (INCLUDING, BUT NOT LIMITED TO, UNIVERSITY COLLEGE LONDON) BE LIABLE 
+   TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL 
+   DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE 
+   AND ITS DOCUMENTATION, EVEN IF THE AUTHOR HAS BEEN ADVISED OF THE 
+   POSSIBILITY OF SUCH DAMAGE.
+   .
+   THE AUTHOR SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT 
+   LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR 
+   A PARTICULAR PURPOSE.  THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" 
+   BASIS, AND THE AUTHOR HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT, 
+   UPDATES, ENHANCEMENTS, OR MODIFICATIONS. 
+
+Files: debian/*
+Copyright: 2013 Steffen Moeller <steffen_moeller at gmx.de>
+License: GPL-2+
+ This package 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.
+ .
+ This package 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/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".

Added: trunk/packages/profit/trunk/debian/docs
===================================================================
--- trunk/packages/profit/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/docs	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1,4 @@
+DOS.txt
+HISTORY
+INSTALL
+00Read.Me

Added: trunk/packages/profit/trunk/debian/patches/AllowReadline.patch
===================================================================
--- trunk/packages/profit/trunk/debian/patches/AllowReadline.patch	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/patches/AllowReadline.patch	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1,15 @@
+Index: profit-3.1/src/Makefile
+===================================================================
+--- profit-3.1.orig/src/Makefile
++++ profit-3.1/src/Makefile
+@@ -6,8 +6,8 @@
+ # To allow use of the GNU Readline library, uncomment the following two
+ # lines - You may need to install the GNU readline development libraries
+ # first!
+-#READLINE    = -DREADLINE_SUPPORT
+-#READLINELIB = -lreadline -lcurses
++READLINE    = -DREADLINE_SUPPORT
++READLINELIB = -lreadline -lcurses
+ 
+ # Uncomment if you want to use the rotate and refit code for avoiding 
+ # local minimum problem. If compiled with gcc -O3 this problem seems to

Added: trunk/packages/profit/trunk/debian/patches/AllowRedundantCleans.patch
===================================================================
--- trunk/packages/profit/trunk/debian/patches/AllowRedundantCleans.patch	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/patches/AllowRedundantCleans.patch	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1,13 @@
+Index: profit-3.1/src/Makefile
+===================================================================
+--- profit-3.1.orig/src/Makefile
++++ profit-3.1/src/Makefile
+@@ -54,7 +54,7 @@
+ 	$(CC) $(COPT) $(READLINE) $(ROTATEREFIT) -o $@ -c $<
+ 
+ clean :
+-	/bin/rm $(OFILES) $(LFILES)
++	/bin/rm -f $(OFILES) $(LFILES)
+ 
+ protos : $(PFILES)
+ 

Added: trunk/packages/profit/trunk/debian/patches/series
===================================================================
--- trunk/packages/profit/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/patches/series	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1,2 @@
+AllowReadline.patch
+AllowRedundantCleans.patch

Added: trunk/packages/profit/trunk/debian/profit-data.dirs
===================================================================
--- trunk/packages/profit/trunk/debian/profit-data.dirs	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/profit-data.dirs	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1 @@
+usr/share/profit

Added: trunk/packages/profit/trunk/debian/profit-data.install
===================================================================
--- trunk/packages/profit/trunk/debian/profit-data.install	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/profit-data.install	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1,2 @@
+mdm78.mat	usr/share/profit/
+ProFit.help	usr/share/profit/

Added: trunk/packages/profit/trunk/debian/profit.dirs
===================================================================
--- trunk/packages/profit/trunk/debian/profit.dirs	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/profit.dirs	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1 @@
+usr/lib/profit

Added: trunk/packages/profit/trunk/debian/profit.install
===================================================================
--- trunk/packages/profit/trunk/debian/profit.install	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/profit.install	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1,2 @@
+src/profit usr/lib/profit/
+debian/profit.sh usr/bin/profit

Added: trunk/packages/profit/trunk/debian/profit.sh
===================================================================
--- trunk/packages/profit/trunk/debian/profit.sh	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/profit.sh	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1,5 @@
+#!/bin/sh
+
+export HELPDIR=/usr/share/profit/
+export DATADIR=/usr/share/profit/
+/usr/lib/profit/profit $*


Property changes on: trunk/packages/profit/trunk/debian/profit.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/profit/trunk/debian/rules
===================================================================
--- trunk/packages/profit/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/rules	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1,20 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+	dh $@ 
+
+override_dh_auto_build:
+	$(MAKE) -C src
+
+override_dh_auto_clean:
+	$(MAKE) -C src clean
+


Property changes on: trunk/packages/profit/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/profit/trunk/debian/source/format
===================================================================
--- trunk/packages/profit/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/profit/trunk/debian/source/format	2013-06-05 16:19:05 UTC (rev 13845)
@@ -0,0 +1 @@
+3.0 (quilt)


