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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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
>>> >> > [email protected]
>>> >> >
>>> >> > To unsubscribe from this list, get a password
>>> >> > reminder, or change your subscription options,
>>> >> > visit the list information page at
>>> >> > https://mail.gna.org/listinfo/relax-users
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