Re: relax 1.3.13/14 oddities -- April 05, 2012 - 15:10

Hi Jack,

I am having extreme difficulty in finding what is wrong here.  I
cannot avoid the memory error message!  I can chase it to a wx Timer
element in something called the relax controller, but that's it.  This
really looks like a broken wxPython install in fink.  The starting
message that we both see:

/sw/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py:14448:
UserWarning: wxPython/wxWidgets release number mismatch
 warnings.warn("wxPython/wxWidgets release number mismatch")

might be indicating the failure point.  wxPython and wxWidgets should
both really be at the same version.  I would guess that the
http://pdb.finkproject.org/pdb/package.php/wxgtk2.8-py27 fink package
(the 2.8.9.1-6 version) is broken.  I am completely stuck and cannot
move further with this problem.  How do we get in contact with the
maintainer of this package?

Sorry,

Edward




On 3 April 2012 13:43, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> Hi,
>
> I think I'll have to do some more testing for this!  Due to my very
> limited access to the Mac I am testing this on, progress will be slow.
>  I will probably need some time to debug relax using the old Mac gtk+
> version of the wx widgets, and will definitely release a new version
> (1.3.15) prior to that.  So maybe it's safe to send out the newer
> relax versions to fink, as the prompt/scripting UI modes function
> perfectly anyway?
>
> Cheers,
>
> Edward
>
>
>
>
> On 2 April 2012 23:04, Jack Howarth <howarth@xxxxxxxxxxxxxxxx> wrote:
> > On Mon, Apr 02, 2012 at 10:18:15PM +0200, Edward d'Auvergne wrote:
> > > Hi Jack,
> > >
> > > I've finally placed the relax-py.info and relax-py.patch files into
> > > /sw/fink/10.4/local/main/finkinfo and installed the 1.3.14 relax
> > > version via fink (with 'fink install relax-py27').  I have to be
> > > careful as I have three different relax installs (the fink one, an svn
> > > copy, and the DMG file version) as well as three different Python
> > > installs (2 from fink and a manual install with Mac framework).  When
> > > I test the GUI with the fink version, my message is:
> > >
> > > $ /sw/bin/python2.7 /sw/bin/relax --gui
> > > /sw/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py:14448:
> > > UserWarning: wxPython/wxWidgets release number mismatch
> > >   warnings.warn("wxPython/wxWidgets release number mismatch")
> > >
> > > ***MEMORY-ERROR***: python2.7[878]: GSlice: assertion failed:
> > > aligned_memory == (gpointer) addr
> > > Abort trap
> > > $
> > >
> > > This is using the 2.8 version of wxPython which fink automatically
> > > installs and which appears to be fatal!  How do I install wxPython 2.9
> > > into the /sw directory without damaging the fink setup?  For my
> > > testing and included in the DMG file, I has used wxPython 2.9.2.4.
> > >
> > > Cheers,
> > >
> > > Edward
> >
> > Edward,
> >    I did a build against Xcode 4.2 on x86_64 fink for darwin10 and
> > it didn't crash. I have...
> >
> > ii  wxgtk2.8                     2.8.10-30                    
> > Cross-platform GUI API - unix/gtk version
> > ii  wxgtk2.8-py27                2.8.9.1-6                    Python 
> > bindings for the wxGTK library
> > ii  wxgtk2.8-shlibs              2.8.10-30                    Shared 
> > libraries for wxgtk2.8-shlibs
> >
> > Did you do a 'fink selfupdate-cvs' and 'fink update-all' to make sure you
> > are getting the lastest packaging?
> >                  Jack
> > ps I get...
> >
> >  relax --gui
> > /sw/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py:14448: 
> > UserWarning: wxPython/wxWidgets release number mismatch
> >  warnings.warn("wxPython/wxWidgets release number mismatch")
> >
> >
> > Thank you for citing:
> >
> >
> > relaxGUI
> > ========
> >
> > Bieri, M., d'Auvergne, E. J. and Gooley, P. R. (2011). relaxGUI: a new 
> > software for fast and simple
> > NMR relaxation data analysis and calculation of ps-ns and micro-s motion 
> > of proteins J. Biomol. NMR,
> > (http://dx.doi.org/10.1007/s10858-011-9509-1).
> >
> >
> >
> > relax
> > =====
> >
> > d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic 
> > models I. Minimisation
> > algorithms and their performance within the model-free and Brownian 
> > rotational diffusion spaces. J.
> > Biomol. NMR, 40(2), 107-119 (http://dx.doi.org/10.1007/s10858-007-9214-2).
> >
> > d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic 
> > models II. A new methodology
> > for the dual optimisation of the model-free parameters and the Brownian 
> > rotational diffusion tensor.
> > J. Biomol. NMR, 40(2), 121-133 
> > (http://dx.doi.org/10.1007/s10858-007-9213-3).
> >
> > > On 26 March 2012 19:54, Jack Howarth <howarth@xxxxxxxxxxxxxxxx> wrote:
> > > > On Mon, Mar 26, 2012 at 07:16:31PM +0200, Edward d'Auvergne wrote:
> > > > > Hi Jack,
> > > > >
> > > > > Thank you for updating this!  From memory, I did see a similar problem
> > > > > when I was using the fink versions of all the software required.
> > > > > Though I also had many problems with dependency clashes with Python,
> > > > > wxPython, numpy, and scipy (note this is different to Scientific
> > > > > Python which is no longer a dependency, see
> > > > > http://pdb.finkproject.org/pdb/package.php/scipy-py27) - I had to use
> > > > > the sources and these different relax dependencies had their own
> > > > > dependencies which were not compatible with each other.  The problem,
> > > > > I think, was the dependance on different gcc versions, so each was
> > > > > taking a day or longer to build as fink kept rebuilding the full tool
> > > > > chain.  Anyway, that's not completely related to this problem and
> > > > > might already be resolved in fink.
> > > > >
> > > > > The problem looks more like a wxPython issue.  Would you be able to
> > > > > tell me the fink repository software and versions you used for this so
> > > > > I can try to replicate the problem?  Do you use the binary
> > > > > distribution archive for the dependencies or have fink compile from
> > > > > the source archives?  I am using XCode 3.2.2, but I don't think using
> > > > > 4.2 will change this problem.  If you had the exact sequence of fink
> > > > > commnds to set the relax dependencies up, that would be appreciated as
> > > > > I could then be sure that I have close to the same setup as you.  Then
> > > > > I could debug and find the exact xwgtk problem, and come up with a
> > > > > special work around.
> > > > >
> > > > > Cheers!
> > > > >
> > > > > Edward
> > > >
> > > > Edward,
> > > >    Try the attached packaging placed in 
> > > > /sw/fink/10.4/local/main/finkinfo. I don't
> > > > know how old your fink installation is. If it is rather old, you might 
> > > > want to consider
> > > > a clean bootstrap following the instructions on 
> > > > http://www.finkproject.org/download/srcdist.php.
> > > > You will want to move aside your current fink installation from /sw to 
> > > > /sw.old beforehand.
> > > > Also make sure you do 'fink selfupdate-cvs' and 'fink update-all' to 
> > > > keep your
> > > > trees and installation current. You should be able to just use 'fink 
> > > > install relax-py27'
> > > > to install relax 1.3.14. I would also consider upgrading your Xcode to 
> > > > 3.2.6 which
> > > > is the last release of the 3.2.x series. Oh, on darwin10, I used the 
> > > > gcc46 compilers
> > > > for the build, when prompted, if that makes any difference.
> > > >                     Jack
> > > > ps I also have built relax 1.3.14 under fink but had to use the 2.9.3 
> > > > release of
> > > > wxPython because that is the only wxPython they have for python 2.7 in 
> > > > macports.
> > > > Have you tested relax against the wxPython 2.9.3 release on linux or 
> > > > any other target?
> > > >
> > > >
> > > >
> > > > > On 26 March 2012 18:14, Jack Howarth <howarth@xxxxxxxxxxxxxxxx> wrote:
> > > > > > Edward,
> > > > > >   I am in the process of updating the relax-py and relax packages in 
> > > > > > fink and
> > > > > > macports to the latest release. However I am seeing some oddities 
> > > > > > with the new
> > > > > > gui interface. In both cases, relax 1.3.13 and 1.3.14 exhibits a bug 
> > > > > > when
> > > > > > executed as 'relax --gui'. The gui interface window opens much 
> > > > > > larger than the
> > > > > > displayed contents. Only if I refresh the window does the contents 
> > > > > > properly
> > > > > > expand out to the actual size of the window (by clicking on the 
> > > > > > green zoom
> > > > > > button in the window frame twice). If I move aside the window, I 
> > > > > > also see a small
> > > > > > square with a butterfly icon left on the screen. This square can't 
> > > > > > be closed or
> > > > > > moved. Running 'relax --test-suite' is even more problematic as it 
> > > > > > seems to
> > > > > > be trapped in an endless loop of display the squares with the 
> > > > > > butterfly icon
> > > > > > and segfaults on exiting...
> > > > > >
> > > > > > % relax --test-suite
> > > > > > /sw/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py:14448:
> > > > > >  UserWarning: wxPython/wxWidgets release number mismatch
> > > > > >  warnings.warn("wxPython/wxWidgets release number mismatch")
> > > > > > Echoing of user function calls has been enabled.
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > #############################
> > > > > > # System / functional tests #
> > > > > > #############################
> > > > > >
> > > > > >
> > > > > > .........................................................................................................................................................................................................................................
> > > > > > ----------------------------------------------------------------------
> > > > > > Ran 233 tests in 291.075s
> > > > > >
> > > > > > OK
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > ##############
> > > > > > # Unit tests #
> > > > > > ##############
> > > > > >
> > > > > >
> > > > > > ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
> > > > > > ----------------------------------------------------------------------
> > > > > > Ran 1232 tests in 11.183s
> > > > > >
> > > > > > OK
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > #############
> > > > > > # GUI tests #
> > > > > > #############
> > > > > >
> > > > > >
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > > .
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > > .
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > >
> > > > > > (python2.7:9037): Gtk-WARNING **: Unable to find default local 
> > > > > > directory monitor type
> > > > > > ..
> > > > > > ----------------------------------------------------------------------
> > > > > > Ran 4 tests in 70.926s
> > > > > >
> > > > > > OK
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > ###################################
> > > > > > # Summary of the relax test suite #
> > > > > > ###################################
> > > > > >
> > > > > >
> > > > > > # Optional packages/modules
> > > > > > ###########################
> > > > > >
> > > > > > No tests skipped due to missing modules.
> > > > > >
> > > > > > # Synopsis
> > > > > > ##########
> > > > > >
> > > > > > System/functional tests ......................................... [ 
> > > > > > OK ]
> > > > > > Unit tests ...................................................... [ 
> > > > > > OK ]
> > > > > > GUI tests ....................................................... [ 
> > > > > > OK ]
> > > > > > Synopsis ........................................................ [ 
> > > > > > OK ]
> > > > > >
> > > > > >
> > > > > >
> > > > > > Segmentation fault
> > > > > >
> > > > > > It is odd that the GUI tests pass but that relax segfaults in the 
> > > > > > process.
> > > > > >                 Jack
> > > > > > ps This is on x86_64 fink under darwin10 using Xcode 4.2.
> > > > > >
> > > > > > _______________________________________________
> > > > > > relax (http://nmr-relax.com)
> > > > > >
> > > > > > This is the relax-users mailing list
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