[Debichem-devel] Bug#703782: Bug#703782: pymol: Unable to launch the Menu

[Michael Banck]

Hi,

On Sun, Mar 24, 2013 at 08:29:01PM +0800, Li Na Zhao wrote:
> On Sun, Mar 24, 2013 at 8:06 PM, Michael Banck <mbanck at debian.org> wrote:
> > On Sun, Mar 24, 2013 at 12:06:06AM +0800, lina wrote:
> >> Package: pymol
> >> Version: 1.5.0.1-2
> >> Severity: normal
> >>
> > Is the problem, that the viewer window ("PyMOL Viewer") appears, but the
> > (detached) window with the menus ("File", "Edit" etc.) called "The PyMOL
> > Molecular Graphics System" does not?  I can not immediately reproduce
> > this here.
> 
> You are right here, "The PyMOL Molecular Graphics System" failed to launch.
> >From the error message:
> 
> File "/usr/lib/python2.7/dist-packages/pymol/__init__.py", line 452,
> in launch_gui
>     sys.modules[self.invocation.options.gui].__init__(self,poll,skin)
> TypeError: module.__init__() takes at most 2 arguments (3 given)
> 
> I checked the __init__.py, it has not been updated or changed recently.
> 
> The problem seems related to the sys.modules, I tried to modify the
> code of the __init__.py, but not work,
> 
> The problem stuck me is that I am not clearly which updated package
> related to it.
> 
> BTW, for your information, due to the urgency of using pymol, I built
> one from svn separately, it works fine.
> but it's isolated from this issue.
 
Hrm, ok.

> I don't know how can you produce this problem, but I can provide a
> list of the packages I installed recently,

So the below installations made the Debian-shipped PyMOL no longer show
the menu window?

> Here it is:
> 
> apt-get install git-core
> apt-get install python-numpy
> apt-get install python-scipy
> apt-get install python-matplotlib
> apt-get install python-dev
> apt-get install python-setuptools
> easy_install -U scikits.statsmodels
> easy_install -U scikit-learn
> easy_install --upgrade pytz
> apt-get install python-dateutil
> easy_install pandas==0.7.3
> apt-get install python-qt4
> apt-get install python-cvxopt
 
My guess would be that one of those easy_install commands messed up your
system with respect to PyMOL.  On the other hand, they do not look very
related to the pymol functionality (but maybe they drag in some
dependencies).  If you know easy_install, you could try to figure out
which modules it installed and see whether you can temporarily disable
them.  TK and PMW would be the prime suspects.

For the record, I installed all the above packages which are being
installed via apt-get and I still cannot reproduce your problem.

It is a lot of work, but you could try to reproduce the problem by
checking with a clean testing system, then running the above
installation (one by one) again to see which one breaks it.


Cheers,

Michael