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

[Jiri Wiesner]

On Sat, 2010-06-12 at 18:14 -0700, Nicholas Breen wrote:
> On Sun, Jun 13, 2010 at 12:11:02AM +0200, Jiri Wiesner wrote:
> > 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.
> 
> That looks much more like a general python problem, not pymol itself.  The most
> immediate guess is a corrupted or missing site.py -- try reinstalling the
> "python2.5" and "python2.5-minimal" packages.
> 
> 
> 

Thank you for a quick answer. I have reinstalled "python2.5" and
"python2.5-minimal", the errors are the same:

iakchos:/home/wiesner# apt-get clean
iakchos:/home/wiesner# aptitude -v reinstall python2.5 python2.5-minimal
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Reading extended state information      
Initializing package states... Done
Reading task descriptions... Done  
The following packages will be REINSTALLED:
  python2.5 python2.5-minimal 
The following partially installed packages will be configured:
  gnochm openoffice.org-emailmerge python-chm python-numpy python-uno 
0 packages upgraded, 0 newly installed, 2 reinstalled, 0 to remove and 0
not upgraded.
Need to get 4327kB of archives. After unpacking 0B will be used.
Writing extended state information... Done
Get:1 http://security.debian.org lenny/updates/main python2.5 2.5.2-15
+lenny1 [3039kB]
Get:2 http://security.debian.org lenny/updates/main python2.5-minimal
2.5.2-15+lenny1 [1287kB]
Fetched 4327kB in 0s (4377kB/s)      
(Reading database ... 120111 files and directories currently installed.)
Preparing to replace python2.5 2.5.2-15+lenny1
(using .../python2.5_2.5.2-15+lenny1_amd64.deb) ...
Unpacking replacement python2.5 ...
Preparing to replace python2.5-minimal 2.5.2-15+lenny1
(using .../python2.5-minimal_2.5.2-15+lenny1_amd64.deb) ...
Unpacking replacement python2.5-minimal ...
Processing triggers for menu ...
Processing triggers for man-db ...
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-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
Setting up python2.5-minimal (2.5.2-15+lenny1) ...
'import site' failed; use -v for traceback
Setting up python2.5 (2.5.2-15+lenny1) ...
'import site' failed; use -v for traceback
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
Processing triggers for menu ...
Errors were encountered while processing:
python-chm
gnochm
python-numpy
python-uno
openoffice.org-emailmerge
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
Reading package lists... Done             
Building dependency tree       
Reading state information... Done
Reading extended state information      
Initializing package states... Done
Reading task descriptions... Done  

Current status: 0 broken [+0], 0 updates [+0], 0 new [+0].
iakchos:/home/wiesner# 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


Downgrading the python2.5, python2.5-dev and python2.5-minimal packages
to the version 2.5.2-15 gives the same errors too.