From: DeLano S. <de...@de...> - 2008-07-22 14:59:47
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Daniel, Any time you see the "import site failed" error from Python, you can infer that there is a problem with the Python interpreter being unable to access its required libraries. Messages after that aren't typically informative. This usually a path configuration issue, but I think it can also happen when there is a version mismatch betweehn the executable the libraries (running python 2.5 executables against 2.4 libraries or vice versa). If using the system-provided Python, you shouldn't have to set PYTHON_HOME since it will have been compiled in by default. Try the following in a new shell: export PYMOL_PATH=/var/lib/python-support/python2.5/pymol/ python2.5 ${PYMOL_PATH}/__init__.py Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:su...@de... -----Original Message----- From: pym...@li... [mailto:pym...@li...] On Behalf Of Daniel Rigden Sent: Tuesday, July 22, 2008 7:39 AM To: pym...@li... Subject: [PyMOL] python/pymol malfunction on new Ubuntu installation Dear all First let me confess that my problem does not just involved pymol. However, it is hampering my use of pymol amongst other things and there must be many python experts who read this list. My problem, on a completely fresh Ubuntu 8.04 install, is that python can find modules when asked to import them. So export PYMOL_PATH=/var/lib/python-support/python2.5/pymol/ export PYTHONHOME=/usr/lib/python2.5 python2.5 ${PYMOL_PATH}/__init__.py gives me 'import site' failed; use -v for traceback Traceback (most recent call last): File "/var/lib/python-support/python2.5/pymol//__init__.py", line 109, in <module> import threading ImportError: No module named threading /usr/lib/python2.5 contains site.py, threading.py and all the rest. Can anyone help? I'd be very grateful. Daniel -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Daniel R. <dr...@li...> - 2008-07-22 16:20:47
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Warren Thanks for that. That's rather what I expected/feared. I'd still be delighted to hear from anyone who may understand why Python isn't working straight out of the box. Best wishes Daniel On Tue, 2008-07-22 at 09:04 -0700, Warren DeLano wrote: > Daniel, > > This kind of complexity illustrates why we distribute standalone binaries for Linux which include their own Python interpreter. In short, there is simply too much heterogenaiety present in the 7+ years worth of deployed Linux distribution / version / package-manager combinations for us to be able to support any one of them individually. > > So to use PyMOL with a system-provided Python on Linux, our recommended approach is to build from the open-source code using the distutils method (python setup.py build install; python setup2.py install; ./pymol). > > However, in this case, it sounds like your system-provided Python may not itself be working, so you may need to work with the Unbuntu folks to straighten that out first. I can assure you that until "python" or "python2.5" alone just works with no errors, there is little chance of PyMOL building or running correctly. > > Cheers, > Warren > > -----Original Message----- > From: pym...@li... [mailto:pym...@li...] On Behalf Of Daniel Rigden > Sent: Tuesday, July 22, 2008 8:25 AM > To: DeLano Scientific > Cc: pym...@li... > Subject: Re: [PyMOL] python/pymol malfunction on new Ubuntu installation > > Warren > > Thanks for the quick reply. I tried what you suggested but I get the same error. > > How can I check how the path has been configured? It seems as if there is only one python so there shouldn't be scope for confusion; I can only find one site.py, for example, in > > /usr/lib/python2.5/site.py > > [I'm assuming /usr/lib64/python2.5/site.py is a link] > > On the other hand, in Synaptic, I see > > python > python2.5 > python2.5-minimal > > all separately listed and installed, which I don;t really understand. > The Installed version of python is 2.5.2-0ubuntu1, while for the others it's 2.5.2-2ubuntu4. > > Thanks again > > Daniel > > On Tue, 2008-07-22 at 07:59 -0700, DeLano Scientific wrote: > > Daniel, > > > > Any time you see the "import site failed" error from Python, you can infer that there is a problem with the Python interpreter being unable to access its required libraries. Messages after that aren't typically informative. > > > > This usually a path configuration issue, but I think it can also happen when there is a version mismatch betweehn the executable the libraries (running python 2.5 executables against 2.4 libraries or vice versa). > > > > If using the system-provided Python, you shouldn't have to set PYTHON_HOME since it will have been compiled in by default. Try the following in a new shell: > > > > export PYMOL_PATH=/var/lib/python-support/python2.5/pymol/ > > python2.5 ${PYMOL_PATH}/__init__.py > > > > Cheers, > > Warren > > -- > > DeLano Scientific LLC > > Subscriber Support Services > > mailto:su...@de... > > > > > > -----Original Message----- > > From: pym...@li... > > [mailto:pym...@li...] On Behalf Of Daniel > > Rigden > > Sent: Tuesday, July 22, 2008 7:39 AM > > To: pym...@li... > > Subject: [PyMOL] python/pymol malfunction on new Ubuntu installation > > > > Dear all > > > > First let me confess that my problem does not just involved pymol. > > However, it is hampering my use of pymol amongst other things and there must be many python experts who read this list. > > > > My problem, on a completely fresh Ubuntu 8.04 install, is that python > > can find modules when asked to import them. So > > > > export PYMOL_PATH=/var/lib/python-support/python2.5/pymol/ > > export PYTHONHOME=/usr/lib/python2.5 > > python2.5 ${PYMOL_PATH}/__init__.py > > > > gives me > > > > 'import site' failed; use -v for traceback Traceback (most recent call last): > > File "/var/lib/python-support/python2.5/pymol//__init__.py", line 109, in <module> > > import threading > > ImportError: No module named threading > > > > > > /usr/lib/python2.5 contains site.py, threading.py and all the rest. > > > > > > Can anyone help? I'd be very grateful. > > > > Daniel > > > -- > Dr Daniel John Rigden Tel:(+44) 151 795 4467 > School of Biological Sciences FAX:(+44) 151 795 4406 > Room 101, Biosciences Building > University of Liverpool > Crown St., > Liverpool L69 7ZB, U.K. > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. |
From: Daniel R. <dr...@li...> - 2008-07-22 15:21:42
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Warren Thanks for the quick reply. I tried what you suggested but I get the same error. How can I check how the path has been configured? It seems as if there is only one python so there shouldn't be scope for confusion; I can only find one site.py, for example, in /usr/lib/python2.5/site.py [I'm assuming /usr/lib64/python2.5/site.py is a link] On the other hand, in Synaptic, I see python python2.5 python2.5-minimal all separately listed and installed, which I don;t really understand. The Installed version of python is 2.5.2-0ubuntu1, while for the others it's 2.5.2-2ubuntu4. Thanks again Daniel On Tue, 2008-07-22 at 07:59 -0700, DeLano Scientific wrote: > Daniel, > > Any time you see the "import site failed" error from Python, you can infer that there is a problem with the Python interpreter being unable to access its required libraries. Messages after that aren't typically informative. > > This usually a path configuration issue, but I think it can also happen when there is a version mismatch betweehn the executable the libraries (running python 2.5 executables against 2.4 libraries or vice versa). > > If using the system-provided Python, you shouldn't have to set PYTHON_HOME since it will have been compiled in by default. Try the following in a new shell: > > export PYMOL_PATH=/var/lib/python-support/python2.5/pymol/ > python2.5 ${PYMOL_PATH}/__init__.py > > Cheers, > Warren > -- > DeLano Scientific LLC > Subscriber Support Services > mailto:su...@de... > > > -----Original Message----- > From: pym...@li... [mailto:pym...@li...] On Behalf Of Daniel Rigden > Sent: Tuesday, July 22, 2008 7:39 AM > To: pym...@li... > Subject: [PyMOL] python/pymol malfunction on new Ubuntu installation > > Dear all > > First let me confess that my problem does not just involved pymol. > However, it is hampering my use of pymol amongst other things and there must be many python experts who read this list. > > My problem, on a completely fresh Ubuntu 8.04 install, is that python can find modules when asked to import them. So > > export PYMOL_PATH=/var/lib/python-support/python2.5/pymol/ > export PYTHONHOME=/usr/lib/python2.5 > python2.5 ${PYMOL_PATH}/__init__.py > > gives me > > 'import site' failed; use -v for traceback Traceback (most recent call last): > File "/var/lib/python-support/python2.5/pymol//__init__.py", line 109, in <module> > import threading > ImportError: No module named threading > > > /usr/lib/python2.5 contains site.py, threading.py and all the rest. > > > Can anyone help? I'd be very grateful. > > Daniel > -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. |