On Monday 25,March,2013 09:01 AM, Michael Banck wrote:
> 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 <mba...@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.
prime --> primary
>
> For the record, I installed all the above packages which are being
> installed via apt-get and I still cannot reproduce your problem.
Sorry for the trouble.
>
> 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.
A very nice suggestion, but I don't have some testing system around, my
Desktop is experiment one, I guess I will test on it within the next 36
hours and get feedback to you. If not work, perhaps we can just put it
aside for a while to see how it's going with the future update.
Thanks again for your help and time,
Best regards,
>
>
> Cheers,
>
> Michael
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