debian/0000755000000000000000000000000011675310525007173 5ustar debian/menu0000644000000000000000000000017011262636072010060 0ustar ?package(mssstest):needs="text" section="Applications/Science/Medicine"\ title="mssstest" command="/usr/bin/mssstest" debian/README.Debian0000644000000000000000000000521411262636072011236 0ustar mssstest for Debian ------------------- 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 ) 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@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@Roxburgh.net.nz Fri Dec 17 12:40:29 2004 To: Steffen Moeller 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@pzr3.pzr.uni-rostock.de] Sent: 02 December 2004 11:25 To: richard@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". [...] debian/manpages0000644000000000000000000000002211262636072010703 0ustar debian/mssstest.1 debian/source/0000755000000000000000000000000011522615464010474 5ustar debian/source/format0000644000000000000000000000001411467561373011711 0ustar 3.0 (quilt) debian/docs0000644000000000000000000000003311262636072010042 0ustar README edss.txt global.dat debian/install0000644000000000000000000000012011262636072010555 0ustar mssstest usr/bin edss.txt usr/share/mssstest global.dat usr/share/mssstest debian/copyright0000644000000000000000000000334211262636072011130 0ustar This package was debianized by Steffen Moeller on Tue, 30 Nov 2004 16:32:26 +0100. It was downloaded from http://www-gene.cimr.cam.ac.uk/MSgenetics/GAMES/MSSS/ Copyright: (C) 2004-2007 Shaun Seaman and Richard Roxburgh Upstream Author: Shaun Seaman and Richard Roxburgh 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. debian/mssstest.10000644000000000000000000000502011262636072011137 0ustar .\" 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 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 .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\fP and .\" \fI\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 . .PP This manual page was written by Steffen Moeller , for the Debian project (but may be used by others). debian/rules0000755000000000000000000000014711675310472010256 0ustar #!/usr/bin/make -f # debian/rules file for mssstest # Andreas Tille , GPL %: dh $@ debian/patches/0000755000000000000000000000000011675307732010630 5ustar debian/patches/10_makefile.patch0000644000000000000000000000057011675307732013730 0ustar --- 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 debian/patches/series0000644000000000000000000000007011675307732012042 0ustar 20_gcc-4.3.patch 10_fixdatapath.patch 10_makefile.patch debian/patches/10_fixdatapath.patch0000644000000000000000000000217711675307732014455 0ustar --- 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> 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); debian/patches/20_gcc-4.3.patch0000644000000000000000000000126011675307732013207 0ustar --- mssstest-3.0.orig/neededroutines.cpp +++ mssstest-3.0/neededroutines.cpp @@ -1,3 +1,4 @@ +#include #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 + #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 +} debian/changelog0000644000000000000000000000471711675310445011057 0ustar mssstest (3.0-3) unstable; urgency=low * Finally removed debian/watch because upstream does not seem to release new versions Closes: #450107 * debian/source/format: 3.0 (quilt) * debian/control: - Standards-Version: 3.9.2 (no changes needed) - Fixed Vcs fields * Debhelper 8 (control+compat) -- Andreas Tille Sat, 24 Dec 2011 09:43:01 +0100 mssstest (3.0-2) unstable; urgency=low * Deactivated debian/watch: Upstream does not use version numbering on downloadable tarball. * debian/control: - Standards-Version: 3.8.3 (added README.source) - Debhelper 7 - Removed cdbs dependency * debian/rules: make use of dh -- Andreas Tille Tue, 06 Oct 2009 14:47:59 +0200 mssstest (3.0-1) unstable; urgency=low * New upstream version * New version can not be obtained via watch file from upstream but just out of the README file inside the archive. Fixed watch file anyway to notice when upstream changed this policy * Group maintenance with permission of maintainer Steffen Möller * 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 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 Tue, 05 May 2005 17:05:26 +0200 mssstest (2.0-1) unstable; urgency=low * Initial Release (Closes:Bug#283695). -- Steffen Moeller Tue, 30 Nov 2004 16:32:26 +0100 debian/compat0000644000000000000000000000000211675310453010371 0ustar 8 debian/control0000644000000000000000000000212711675310503010574 0ustar Source: mssstest Section: non-free/science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Steffen Moeller , Andreas Tille Build-Depends: debhelper (>= 8) Standards-Version: 3.9.2 Homepage: http://www-gene.cimr.cam.ac.uk/MSgenetics/GAMES/MSSS/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mssstest/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mssstest/trunk/ XS-Autobuild: yes Package: mssstest Architecture: any Depends: ${shlibs:Depends}, ${misc: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.