[med-svn] r2273 - in trunk/packages/mssstest/trunk/debian: . patches
tille at alioth.debian.org
tille at alioth.debian.org
Mon Jul 21 12:51:22 UTC 2008
Author: tille
Date: 2008-07-21 12:51:20 +0000 (Mon, 21 Jul 2008)
New Revision: 2273
Added:
trunk/packages/mssstest/trunk/debian/install
trunk/packages/mssstest/trunk/debian/patches/
trunk/packages/mssstest/trunk/debian/patches/10_fixdatapath.patch
trunk/packages/mssstest/trunk/debian/patches/10_makefile.patch
trunk/packages/mssstest/trunk/debian/patches/20_gcc-4.3.patch
trunk/packages/mssstest/trunk/debian/patches/series
Removed:
trunk/packages/mssstest/trunk/debian/dirs
trunk/packages/mssstest/trunk/debian/mssstest.sh
Modified:
trunk/packages/mssstest/trunk/debian/README.Debian
trunk/packages/mssstest/trunk/debian/changelog
trunk/packages/mssstest/trunk/debian/control
trunk/packages/mssstest/trunk/debian/copyright
trunk/packages/mssstest/trunk/debian/menu
trunk/packages/mssstest/trunk/debian/mssstest.1
trunk/packages/mssstest/trunk/debian/rules
Log:
Several changes to build new upstream version with gcc-4.3 successfully
Modified: trunk/packages/mssstest/trunk/debian/README.Debian
===================================================================
--- trunk/packages/mssstest/trunk/debian/README.Debian 2008-07-21 09:53:50 UTC (rev 2272)
+++ trunk/packages/mssstest/trunk/debian/README.Debian 2008-07-21 12:51:20 UTC (rev 2273)
@@ -1,13 +1,12 @@
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 orignal source is seeking for two files edss.txt and global.dat
+in the current directory. Under Debian these files were moved to
+/usr/share/mssstest and the code was adjusted. I do not think that
+this change conflicts with the license (Andreas Tille <tille at debian.org>)
+Please use the bug reporting tool reportbug to report any problems with
+this change. Alternatively you can mail the maintainer of this package.
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
Modified: trunk/packages/mssstest/trunk/debian/changelog
===================================================================
--- trunk/packages/mssstest/trunk/debian/changelog 2008-07-21 09:53:50 UTC (rev 2272)
+++ trunk/packages/mssstest/trunk/debian/changelog 2008-07-21 12:51:20 UTC (rev 2273)
@@ -1,4 +1,4 @@
-mssstest (3.0-1) UNRELEASED; urgency=low
+mssstest (3.0-1) unstable; urgency=low
* New upstream version
* New version can not be obtained via watch file from upstream
@@ -8,6 +8,18 @@
* Moved manpage and wrapper script to debian directory
* Added Homepage field
* Standards-Version: 3.8.0 (no changes needed)
+ * Vcs fields
+ * XS-Autobuild: yes
+ * No versioned debhelper dependency
+ * Use quilt and cdbs
+ * Fix gcc-4.3 problem
+ * Use explicite path /usr/share/mssstest to the data files instead
+ requiring the user to have these files in the local directory.
+ This step was documented in README.Debian. As a consequence
+ mssstest.sh was removed because it is not needed any more
+ * Patch makefile to get the name of resulting executable in lower
+ cases and without .exe extension
+ * debian/menu: Applications/Science/Medicine
-- Andreas Tille <tille at debian.org> Sun, 20 Jul 2008 21:51:26 +0200
Modified: trunk/packages/mssstest/trunk/debian/control
===================================================================
--- trunk/packages/mssstest/trunk/debian/control 2008-07-21 09:53:50 UTC (rev 2272)
+++ trunk/packages/mssstest/trunk/debian/control 2008-07-21 12:51:20 UTC (rev 2273)
@@ -3,11 +3,14 @@
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>,
+Uploaders: Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 4.0.0)
+Build-Depends: debhelper, cdbs, quilt
Standards-Version: 3.8.0
Homepage: http://www-gene.cimr.cam.ac.uk/MSgenetics/GAMES/MSSS/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mssstest/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mssstest/trunk/
+XS-Autobuild: yes
Package: mssstest
Architecture: any
@@ -19,5 +22,3 @@
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/
Modified: trunk/packages/mssstest/trunk/debian/copyright
===================================================================
--- trunk/packages/mssstest/trunk/debian/copyright 2008-07-21 09:53:50 UTC (rev 2272)
+++ trunk/packages/mssstest/trunk/debian/copyright 2008-07-21 12:51:20 UTC (rev 2273)
@@ -3,7 +3,7 @@
It was downloaded from http://www-gene.cimr.cam.ac.uk/MSgenetics/GAMES/MSSS/
-Copyright:
+Copyright: (C) 2004-2007 Shaun Seaman and Richard Roxburgh
Upstream Author: Shaun Seaman and Richard Roxburgh <richard at Roxburgh.net.nz>
Deleted: trunk/packages/mssstest/trunk/debian/dirs
===================================================================
--- trunk/packages/mssstest/trunk/debian/dirs 2008-07-21 09:53:50 UTC (rev 2272)
+++ trunk/packages/mssstest/trunk/debian/dirs 2008-07-21 12:51:20 UTC (rev 2273)
@@ -1,4 +0,0 @@
-usr/bin
-usr/lib/mssstest
-usr/share/mssstest
-usr/share/doc/mssstest
Added: trunk/packages/mssstest/trunk/debian/install
===================================================================
--- trunk/packages/mssstest/trunk/debian/install (rev 0)
+++ trunk/packages/mssstest/trunk/debian/install 2008-07-21 12:51:20 UTC (rev 2273)
@@ -0,0 +1,4 @@
+mssstest usr/bin
+edss.txt usr/share/mssstest
+global.dat usr/share/mssstest
+
Modified: trunk/packages/mssstest/trunk/debian/menu
===================================================================
--- trunk/packages/mssstest/trunk/debian/menu 2008-07-21 09:53:50 UTC (rev 2272)
+++ trunk/packages/mssstest/trunk/debian/menu 2008-07-21 12:51:20 UTC (rev 2273)
@@ -1,2 +1,2 @@
-?package(mssstest):needs="text" section="Apps/Science"\
+?package(mssstest):needs="text" section="Applications/Science/Medicine"\
title="mssstest" command="/usr/bin/mssstest"
Modified: trunk/packages/mssstest/trunk/debian/mssstest.1
===================================================================
--- trunk/packages/mssstest/trunk/debian/mssstest.1 2008-07-21 09:53:50 UTC (rev 2272)
+++ trunk/packages/mssstest/trunk/debian/mssstest.1 2008-07-21 12:51:20 UTC (rev 2273)
@@ -19,13 +19,25 @@
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.
+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.
+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.
+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,
@@ -35,7 +47,7 @@
and "indivmsss.out".
.SH SEE ALSO
http://www-gene.cimr.cam.ac.uk/MSgenetics/GAMES/MSSS/#top
-.br.
+.br
/usr/share/doc/mssstest/README.gz
.SH AUTHOR
mssstest was written by Shaun Seaman and Richard Roxburgh <Richard at Roxburgh.net.nz>.
Deleted: trunk/packages/mssstest/trunk/debian/mssstest.sh
===================================================================
--- trunk/packages/mssstest/trunk/debian/mssstest.sh 2008-07-21 09:53:50 UTC (rev 2272)
+++ trunk/packages/mssstest/trunk/debian/mssstest.sh 2008-07-21 12:51:20 UTC (rev 2273)
@@ -1,12 +0,0 @@
-#!/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/patches/10_fixdatapath.patch
===================================================================
--- trunk/packages/mssstest/trunk/debian/patches/10_fixdatapath.patch (rev 0)
+++ trunk/packages/mssstest/trunk/debian/patches/10_fixdatapath.patch 2008-07-21 12:51:20 UTC (rev 2273)
@@ -0,0 +1,37 @@
+--- mssstest-3.0.orig/roxburgh.cpp
++++ mssstest-3.0/roxburgh.cpp
+@@ -110,16 +110,16 @@
+ float temp;
+ int errorflag1, errorflag2;
+
+- cout << "Reading data file `edss.txt'.\n";
++ cout << "Reading data file `/usr/share/mssstest/edss.txt'.\n";
+
+ for (i=0; i<MAXGROUPS; i++)
+ usegroup[i] = 0;
+
+ i = 0;
+
+- ifstream fin("edss.txt");
++ ifstream fin("/usr/share/mssstest/edss.txt");
+ if (!fin)
+- {cout << "Cannot find file `edss.txt'." << endl;
++ {cout << "Cannot find file `/usr/share/mssstest/edss.txt'." << endl;
+ cout << "Type 0 and return to end program\n";
+ cin >> key;
+ exit(0);
+@@ -204,11 +204,11 @@
+ int i, j, key, durtemp, edsstemp;
+ float mssstable[20][31];
+
+- cout << "Reading global MSSS file `global.dat'.\n";
++ cout << "Reading global MSSS file `/usr/share/mssstest/global.dat'.\n";
+
+- ifstream fin("global.dat");
++ ifstream fin("/usr/share/mssstest/global.dat");
+ if (!fin)
+- {cout << "Cannot find file `global.dat'." << endl;
++ {cout << "Cannot find file `/usr/share/mssstest/global.dat'." << endl;
+ cout << "Type 0 and return to end program\n";
+ cin >> key;
+ exit(0);
Added: trunk/packages/mssstest/trunk/debian/patches/10_makefile.patch
===================================================================
--- trunk/packages/mssstest/trunk/debian/patches/10_makefile.patch (rev 0)
+++ trunk/packages/mssstest/trunk/debian/patches/10_makefile.patch 2008-07-21 12:51:20 UTC (rev 2273)
@@ -0,0 +1,19 @@
+--- mssstest-3.0.orig/makefile
++++ mssstest-3.0/makefile
+@@ -2,8 +2,8 @@
+ mi = neededroutines
+
+
+-MSSStest.exe: $(mi).o $(mu).o
+- g++ -g -o MSSStest.exe $(mi).o $(mu).o -lm -lc
++mssstest: $(mi).o $(mu).o
++ g++ -g -o mssstest $(mi).o $(mu).o -lm -lc
+
+
+ $(mi).o: $(mi).cpp $(mi).h
+@@ -12,3 +12,5 @@
+ $(mu).o: $(mu).cpp
+ g++ -c $(mu).cpp -g -o $(mu).o
+
++clean:
++ rm -f *.o
Added: trunk/packages/mssstest/trunk/debian/patches/20_gcc-4.3.patch
===================================================================
--- trunk/packages/mssstest/trunk/debian/patches/20_gcc-4.3.patch (rev 0)
+++ trunk/packages/mssstest/trunk/debian/patches/20_gcc-4.3.patch 2008-07-21 12:51:20 UTC (rev 2273)
@@ -0,0 +1,29 @@
+--- mssstest-3.0.orig/neededroutines.cpp
++++ mssstest-3.0/neededroutines.cpp
+@@ -1,3 +1,4 @@
++#include <cstdlib>
+ #include "neededroutines.h"
+
+ float gammln(float xx)
+@@ -327,4 +328,4 @@
+ exit(0);
+ }
+ *gammcf = exp(-x+a*log(x)-(*gln))*h;
+-}
+\ No newline at end of file
++}
+--- mssstest-3.0.orig/roxburgh.cpp
++++ mssstest-3.0/roxburgh.cpp
+@@ -1,3 +1,5 @@
++#include <cstdlib>
++
+ #include "neededroutines.h"
+
+ const int MAXPERSON = 20000;
+@@ -466,4 +468,4 @@
+ fout << familynov[i] << "\t" << indivnov[i] << "\t" << edssv[i]*0.5 << "\t" << durationv[i] << "\t" << groupv[i] << "\t" << setprecision(4) << msssv[i] << endl;
+
+ fout.close();
+-}
+\ No newline at end of file
++}
Added: trunk/packages/mssstest/trunk/debian/patches/series
===================================================================
--- trunk/packages/mssstest/trunk/debian/patches/series (rev 0)
+++ trunk/packages/mssstest/trunk/debian/patches/series 2008-07-21 12:51:20 UTC (rev 2273)
@@ -0,0 +1,3 @@
+20_gcc-4.3.patch
+10_fixdatapath.patch
+10_makefile.patch
Modified: trunk/packages/mssstest/trunk/debian/rules
===================================================================
--- trunk/packages/mssstest/trunk/debian/rules 2008-07-21 09:53:50 UTC (rev 2272)
+++ trunk/packages/mssstest/trunk/debian/rules 2008-07-21 12:51:20 UTC (rev 2273)
@@ -1,78 +1,9 @@
#!/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.
+# debian/rules file for mssstest
+# Andreas Tille <tille at debian.org>, GPL
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
-
-
-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
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