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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