Hi,
Ok, this is bad, the error is clearly here in fink:
http://fink.cvs.sourceforge.net/fink/dists/10.4/stable/main/finkinfo/languages/wxgtk2.8-py.info?view=markup.
Specifically the lines:
-----
Package: wxgtk2.8-py%type_pkg[python]
Version: 2.8.9.1
-----
and:
-----
wxgtk2.8 (>=2.8.10-24),
-----
This is wxPython 2.8.9.1 running with wxGTK 2.8.10-24 (or higher) -
that cannot work. The versions need to match. Maybe fixing this
wxPython/wxGTK problem within fink will eliminate the problems for the
fink install of relax (but unfortunately not the relax Application in
the DMG image file that others are seeing).
Regards,
Edward
On 5 April 2012 15:09, Edward d'Auvergne <[email protected]> wrote:
> 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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