[Debichem-devel] Bug#585671: Pymol does not start, errors in python 2.5

[Jiri Wiesner]

Package: pymol
Version: 1.1-1
Severity: important

  
Hello,
it is not possible to run pymol. The execution ends with some python related error (see below). My reportbug package does not work either, hence I'm reporting the bug through email.
Kind regards and thank you very much for maintaining pymol.

Jiri Wiesner




Error:

wiesner at iakchos:~$ pymol 
'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "/var/lib/python-support/python2.5/pymol//__init__.py", line 32, in <module>
    from copy import deepcopy
ImportError: No module named copy




Other important facts:

The following packages are not instalable:
  python-chm
  python-uno
  openoffice.org-emailmerge
  gnochm

This is the error:

Setting up python-chm (0.8.4-0.1+b1) ...
'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "/usr/sbin/update-python-modules", line 7, in <module>
    import sys,os,shutil
ImportError: No module named os
dpkg: error processing python-chm (--configure):
 subprocess post-installation script returned error exit status 1
dpkg: dependency problems prevent configuration of gnochm:
 gnochm depends on python-chm (>= 0.8.2-2); however:
  Package python-chm is not configured yet.
dpkg: error processing gnochm (--configure):
 dependency problems - leaving unconfigured
Setting up python-uno (1:2.4.1+dfsg-1+lenny7) ...
'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "/usr/bin/pycentral", line 3, in <module>
    import fnmatch, glob, os, re, string, sys, time, cStringIO
ImportError: No module named fnmatch
dpkg: error processing python-uno (--configure):
 subprocess post-installation script returned error exit status 1
dpkg: dependency problems prevent configuration of openoffice.org-emailmerge:
 openoffice.org-emailmerge depends on python-uno; however:
  Package python-uno is not configured yet.
dpkg: error processing openoffice.org-emailmerge (--configure):
 dependency problems - leaving unconfigured
Setting up python-numpy (1:1.1.0-3+lenny1) ...
'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "/usr/bin/pycentral", line 3, in <module>
    import fnmatch, glob, os, re, string, sys, time, cStringIO
ImportError: No module named fnmatch
dpkg: error processing python-numpy (--configure):
 subprocess post-installation script returned error exit status 1
Errors were encountered while processing:
 python-chm
 gnochm
 python-uno
 openoffice.org-emailmerge
 python-numpy
E: Sub-process /usr/bin/dpkg returned an error code (1)
A package failed to install.  Trying to recover:
Setting up python-chm (0.8.4-0.1+b1) ...
'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "/usr/sbin/update-python-modules", line 7, in <module>
    import sys,os,shutil
ImportError: No module named os
dpkg: error processing python-chm (--configure):
 subprocess post-installation script returned error exit status 1
Setting up python-uno (1:2.4.1+dfsg-1+lenny7) ...
'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "/usr/bin/pycentral", line 3, in <module>
    import fnmatch, glob, os, re, string, sys, time, cStringIO
ImportError: No module named fnmatch
dpkg: error processing python-uno (--configure):
 subprocess post-installation script returned error exit status 1
dpkg: dependency problems prevent configuration of openoffice.org-emailmerge:
 openoffice.org-emailmerge depends on python-uno; however:
  Package python-uno is not configured yet.
dpkg: error processing openoffice.org-emailmerge (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of gnochm:
 gnochm depends on python-chm (>= 0.8.2-2); however:
  Package python-chm is not configured yet.
dpkg: error processing gnochm (--configure):
 dependency problems - leaving unconfigured
Errors were encountered while processing:
 python-chm
 python-uno
 openoffice.org-emailmerge
 gnochm
Press return to continue.


Package reportbug doesn't work either:

wiesner at iakchos:~$ reportbug 
'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "/usr/bin/reportbug", line 30, in <module>
    import sys, os
ImportError: No module named os


All this suggests some error somewhere deep in python, but I'm not experienced enough to resolve it.


I am using Debian GNU/Linux 5.0.4, amd64 architecture, kernel 2.6.26-22lenny1 and 2.7-18lenny4.
I'm using fully up-to-date Debian stable.