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 _______________________________________________ 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
