[med-svn] r2271 - in trunk/packages: . mssstest mssstest/trunk mssstest/trunk/debian
tille at alioth.debian.org
tille at alioth.debian.org
Sun Jul 20 19:56:05 UTC 2008
Author: tille
Date: 2008-07-20 19:56:04 +0000 (Sun, 20 Jul 2008)
New Revision: 2271
Added:
trunk/packages/mssstest/
trunk/packages/mssstest/trunk/
trunk/packages/mssstest/trunk/debian/
trunk/packages/mssstest/trunk/debian/README.Debian
trunk/packages/mssstest/trunk/debian/changelog
trunk/packages/mssstest/trunk/debian/compat
trunk/packages/mssstest/trunk/debian/control
trunk/packages/mssstest/trunk/debian/copyright
trunk/packages/mssstest/trunk/debian/dirs
trunk/packages/mssstest/trunk/debian/docs
trunk/packages/mssstest/trunk/debian/manpages
trunk/packages/mssstest/trunk/debian/menu
trunk/packages/mssstest/trunk/debian/mssstest.1
trunk/packages/mssstest/trunk/debian/mssstest.sh
trunk/packages/mssstest/trunk/debian/rules
trunk/packages/mssstest/trunk/debian/watch
Log:
Put mssstest under group maintenance with permission of Steffen M?\195?\182ller. This is not yet ready for upload - just an initial injection.
Added: trunk/packages/mssstest/trunk/debian/README.Debian
===================================================================
--- trunk/packages/mssstest/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/mssstest/trunk/debian/README.Debian 2008-07-20 19:56:04 UTC (rev 2271)
@@ -0,0 +1,71 @@
+mssstest for Debian
+-------------------
+
+Upstream has not implemented what one would call an intuitive user
+interface. Please read the upstream README and copy/link the global.dat
+files to the current directory prior to use. Also you need a file with
+patients scores that should be investigated named edss.txt. The shell
+script /usr/bin/mssstest changes the path to /usr/share/mssstest prior
+to execution in order to find these files. The real binary is in
+/usr/lib/mssstest which you might decide to use directly.
+
+The C source code is very clear. Please provide patches to improve the
+user interface if you have spare resources. As Goran weinholt at debian.org
+rightously pointed out, the license does not allow any such modifications,
+though it is my firm belief, that this is of a mere shift in focus of
+the upstream fellows who just see people dying and want to help. I heard
+from multiple directions that these guys are actually nice, even if they
+did not get to me with respect with our problems with this license.
+
+In order to eventually close the bug I have attached our original email
+exchange and removed the tiny changes to the upstream's makefile.
+
+Steffen Möller
+
+
+
+From Richard at Roxburgh.net.nz Fri Dec 17 12:40:29 2004
+To: Steffen Moeller <moeller at pzr3.pzr.uni-rostock.de>
+Subject: RE: MSSStest, request for preprint
+
+Dear Steffen
+
+Thanks for your interest in MSSStest. It's great to have the paper finally
+accepted by Neurology and we are very proud of our little program.
+
+We are also flattered by your interest in distributing it as part of the
+Debian database. However, I am far from clear why anyone would want to buy
+it at a new stand etc when its so readily available for download for free
+and I'm pretty sure that people will be able to find it pretty easily by
+just putting MSSStest into Google.
+
+I enclose the preprint that you requested.
+
+Regards
+
+Richard
+
+
+
+-----Original Message-----
+From: Steffen Moeller [mailto:moeller at pzr3.pzr.uni-rostock.de]
+Sent: 02 December 2004 11:25
+To: richard at roxburgh.net.nz
+Subject: MSSStest, request for preprint
+
+
+[...]
+
+I personally wanted to spread this idea, also for its application to
+other diseases. You tool will therefore appear in the Debian Linux
+distribution in not too far future. I thought this would be of your
+interest. It is a pity that you do not allow the program to be sold. The
+Debian CDs are sold, mostly together with a Computer magazine at a news
+stand for a few Euros.
+
+I am certain that you did not want to prohibit the distribution of your
+software via such channels. If you could remove this clause then at least
+Debian would be helped to provide the package on all the 11 Platforms it
+supports which it would not do for packages it interprets as "non-free".
+
+[...]
Added: trunk/packages/mssstest/trunk/debian/changelog
===================================================================
--- trunk/packages/mssstest/trunk/debian/changelog (rev 0)
+++ trunk/packages/mssstest/trunk/debian/changelog 2008-07-20 19:56:04 UTC (rev 2271)
@@ -0,0 +1,29 @@
+mssstest (2.0-3) UNRELEASED; urgency=low
+
+ * Group maintenance with permission of maintainer Steffen Möller
+ * Moved manpage and wrapper script to debian directory
+
+ -- Andreas Tille <tille at debian.org> Sun, 20 Jul 2008 21:51:26 +0200
+
+mssstest (2.0-2) unstable; urgency=low
+
+ * Reacting on bug report (Closes:Bug#292339)
+ - No modifying upstream source.
+ - Adding email indirectly proving upstream to agree
+ with a distribution of MSSStest with Debian.
+
+ * Moved some files from /usr/share/doc/mssstest
+ to /usr/share/mssstest, binary now located in
+ /usr/lib/mssstest.
+
+ * Provided wrapper to start binary in /usr/lib/mssstest
+ from /usr/bin/mssstest.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Tue, 05 May 2005 17:05:26 +0200
+
+mssstest (2.0-1) unstable; urgency=low
+
+ * Initial Release (Closes:Bug#283695).
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Tue, 30 Nov 2004 16:32:26 +0100
+
Added: trunk/packages/mssstest/trunk/debian/compat
===================================================================
--- trunk/packages/mssstest/trunk/debian/compat (rev 0)
+++ trunk/packages/mssstest/trunk/debian/compat 2008-07-20 19:56:04 UTC (rev 2271)
@@ -0,0 +1 @@
+4
Added: trunk/packages/mssstest/trunk/debian/control
===================================================================
--- trunk/packages/mssstest/trunk/debian/control (rev 0)
+++ trunk/packages/mssstest/trunk/debian/control 2008-07-20 19:56:04 UTC (rev 2271)
@@ -0,0 +1,22 @@
+Source: mssstest
+Section: non-free/science
+Priority: optional
+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>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 4.0.0)
+Standards-Version: 3.6.1
+
+Package: mssstest
+Architecture: any
+Depends: ${shlibs:Depends}
+Description: Normalisation of disease scores for patients with Multiple Sclerosis
+ MSSStest is a program for implementing the method described in the
+ article The Multiple Sclerosis Severity Score. R. Roxburgh S. Seaman et
+ al. (2004), accepted for publication by Neurology. It calculates MSSS
+ scores and uses these scores to test for differences between disease
+ progression rates in different groups defined by genotype at some locus. A
+ brief description of the method is given below.
+ .
+ Homepage: http://www-gene.cimr.cam.ac.uk/MSgenetics/GAMES/MSSS/
Added: trunk/packages/mssstest/trunk/debian/copyright
===================================================================
--- trunk/packages/mssstest/trunk/debian/copyright (rev 0)
+++ trunk/packages/mssstest/trunk/debian/copyright 2008-07-20 19:56:04 UTC (rev 2271)
@@ -0,0 +1,38 @@
+This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
+Tue, 30 Nov 2004 16:32:26 +0100.
+
+It was downloaded from http://www-gene.cimr.cam.ac.uk/MSgenetics/GAMES/MSSS/
+
+Copyright:
+
+Upstream Author: Shaun Seaman and Richard Roxburgh <richard at Roxburgh.net.nz>
+
+License:
+
+Licensing of MSSStest
+=====================
+
+This software is downloaded at the user's risk. Anyone may copy it but
+no one may sell it.
+
+We make no representation or warranties with respect to the MSSStest
+software and specifically disclaim any implied warranties of
+merchantability and fitness for a particular purpose. We reserve the
+right to revise the MSSStest software and to make changes therein from
+time to time without obligation to notify any person or organisation of
+such revision or changes. While we make every effort to ensure the
+reliability of the MSSStest software we may not be held responsible for
+errors, omissions or other inaccuracies or any consequences thereof.
+
+THIS SOFTWARE IS PROVIDED ``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 SHAUN SEAMAN OR RICHARD ROXBURGH OR THEIR EMPLOYERS 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: trunk/packages/mssstest/trunk/debian/dirs
===================================================================
--- trunk/packages/mssstest/trunk/debian/dirs (rev 0)
+++ trunk/packages/mssstest/trunk/debian/dirs 2008-07-20 19:56:04 UTC (rev 2271)
@@ -0,0 +1,4 @@
+usr/bin
+usr/lib/mssstest
+usr/share/mssstest
+usr/share/doc/mssstest
Added: trunk/packages/mssstest/trunk/debian/docs
===================================================================
--- trunk/packages/mssstest/trunk/debian/docs (rev 0)
+++ trunk/packages/mssstest/trunk/debian/docs 2008-07-20 19:56:04 UTC (rev 2271)
@@ -0,0 +1,3 @@
+README
+edss.txt
+global.dat
Added: trunk/packages/mssstest/trunk/debian/manpages
===================================================================
--- trunk/packages/mssstest/trunk/debian/manpages (rev 0)
+++ trunk/packages/mssstest/trunk/debian/manpages 2008-07-20 19:56:04 UTC (rev 2271)
@@ -0,0 +1 @@
+debian/mssstest.1
Added: trunk/packages/mssstest/trunk/debian/menu
===================================================================
--- trunk/packages/mssstest/trunk/debian/menu (rev 0)
+++ trunk/packages/mssstest/trunk/debian/menu 2008-07-20 19:56:04 UTC (rev 2271)
@@ -0,0 +1,2 @@
+?package(mssstest):needs="text" section="Apps/Science"\
+ title="mssstest" command="/usr/bin/mssstest"
Added: trunk/packages/mssstest/trunk/debian/mssstest.1
===================================================================
--- trunk/packages/mssstest/trunk/debian/mssstest.1 (rev 0)
+++ trunk/packages/mssstest/trunk/debian/mssstest.1 2008-07-20 19:56:04 UTC (rev 2271)
@@ -0,0 +1,44 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH MSSSTEST 1 "November 30, 2004"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+mssstest \- Normalisationo of disease scores - originally developed for the EDSS for Multiple Sclerosis
+.SH SYNOPSIS
+.B mssstest
+.br
+.SH DESCRIPTION
+Suppose one is interested in determining whether the genotype at some locus of interest affects the rate of progression of disease of people with Multiple Sclerosis (MS). One method would be to calculate the mean EDSS score in patients with each of the genotypes and test whether they are significantly different. However, this approach is inefficient if patients have their EDSS assessed at different durations of disease, as patients who have had MS longer typically have higher EDSS scores regardless of their genotype. By adjusting for duration, a more powerful test can be developed.
+.br
+MSSStest is a program for implementing the method described in the article The Multiple Sclerosis Severity Score. R. Roxburgh S. Seaman et al. (2004), accepted for publication by Neurology. It calculates MSSS scores and uses these scores to test for differences between disease progression rates in different groups defined by genotype at some locus.
+.br
+To use the program first copy the table of disease scores to the current directory. You are expected to use the EDSS scores provided by the authors.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+.SH OPTIONS
+The program does not accept options, it should, though. The output goes to the files "msss.out"
+and "indivmsss.out".
+.SH SEE ALSO
+http://www-gene.cimr.cam.ac.uk/MSgenetics/GAMES/MSSS/#top
+.br.
+/usr/share/doc/mssstest/README.gz
+.SH AUTHOR
+mssstest was written by Shaun Seaman and Richard Roxburgh <Richard at Roxburgh.net.nz>.
+.PP
+This manual page was written by Steffen Moeller <moeller at pzr.uni-rostock.de>,
+for the Debian project (but may be used by others).
Added: trunk/packages/mssstest/trunk/debian/mssstest.sh
===================================================================
--- trunk/packages/mssstest/trunk/debian/mssstest.sh (rev 0)
+++ trunk/packages/mssstest/trunk/debian/mssstest.sh 2008-07-20 19:56:04 UTC (rev 2271)
@@ -0,0 +1,12 @@
+#!/bin/sh
+
+# I was told that the official license does not
+# allow me to change the upstream source .. well.
+
+if [ ! -w . ]; then
+ echo Need write access to current directory.
+ exit -1
+fi
+
+ln -sf /usr/share/mssstest/edss.txt /usr/share/mssstest/global.dat . && /usr/lib/mssstest/mssstest $* && rm edss.txt global.dat
+
Added: trunk/packages/mssstest/trunk/debian/rules
===================================================================
--- trunk/packages/mssstest/trunk/debian/rules (rev 0)
+++ trunk/packages/mssstest/trunk/debian/rules 2008-07-20 19:56:04 UTC (rev 2271)
@@ -0,0 +1,78 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+configure: configure-stamp
+configure-stamp:
+ dh_testdir
+ # Add here commands to configure the package.
+
+ touch configure-stamp
+
+
+build: build-stamp
+
+BINARY=mssstest
+build-stamp: configure-stamp
+ dh_testdir
+ g++ $(CFLAGS) -o $(BINARY) *.cpp -lm -lc
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp
+ rm -f $(BINARY) *.o
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+ cp $(BINARY) $(CURDIR)/debian/mssstest/usr/lib/mssstest/
+ cp debian/mssstest.sh $(CURDIR)/debian/mssstest/usr/bin/mssstest
+ cp edss.txt global.dat $(CURDIR)/debian/mssstest/usr/share/mssstest/
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installmenu
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure
Property changes on: trunk/packages/mssstest/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/mssstest/trunk/debian/watch
===================================================================
--- trunk/packages/mssstest/trunk/debian/watch (rev 0)
+++ trunk/packages/mssstest/trunk/debian/watch 2008-07-20 19:56:04 UTC (rev 2271)
@@ -0,0 +1,6 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# Site Directory Pattern Version Script
+version=2
+http://www-gene.cimr.cam.ac.uk MSgenetics/GAMES/MSSS MSSStest[.-]?(.*)\.tar.gz debian uupdate
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