Hi again,<br><br>Just read the rest of the thread, two points (one pedantic):<br><br>1. Did you install on OS X with macports? Make sure that the directories you are adding to your PYTHONPATH variable exist, ie run "ls /usr/local/lib/python" in a shell and make sure the directories you are adding are present.<br>
<br>2. Will is right, it's been awhile since I wore my sysadmin hat and I
messed up the order of .bashrc and .bash_profile. Edit .bash_profile or
just .profile since those are processed when the shell is invoked
non-interactively while .bashrc is not.<br>
<br>
Speaking of that, does anyone have startup scripts for omero? If not would it be useful to add them to the package?<br>Cheers,<br>jmw<br><br><div class="gmail_quote">On Sat, Dec 12, 2009 at 9:25 AM, Will Moore <span dir="ltr"><<a href="mailto:will@lifesci.dundee.ac.uk">will@lifesci.dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div style="word-wrap: break-word;"><div>Hi,</div><div><br></div>This page has some easier instructions for Mac, which may help with PYTHONPATH issues. <div>
<a href="http://www.openmicroscopy.org.uk/site/support/omero4/server/install-omero-4.1-on-mac-os-x-10.5" target="_blank">http://www.openmicroscopy.org.uk/site/support/omero4/server/install-omero-4.1-on-mac-os-x-10.5</a></div>
<div>It describes editing the .bash_profile which achieves much the same as .bashrc.</div><div><br><div>The nano .bashrc command described below should be run when you are in the /User/user_name/ directory (on a Mac at least). Not sure how that relates to Unix. </div>
<div class="im"><div><br></div><div><blockquote type="cite"><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">I ran echo $PYTHONPATH and got '/opt/Ice-3.3/python:</blockquote></blockquote></blockquote>
</div></blockquote></div><div><br></div></div><div>Just make sure that is the right path. Not </div><div>/Ice-3.3.1/</div><div>since you say you are using Ice-3.3.1 ?</div><div><br></div><div> Hope that helps,</div><div><br>
</div><font color="#888888"><div> Will.</div></font><div><div></div><div class="h5"><div><br></div><div><br><div><div>On 12 Dec 2009, at 16:59, John Wallach wrote:</div><br><blockquote type="cite">I can't speak to whether you can upgrade directly but you should be able to make sure your pythonpath is set correctly pretty easily. Edit the .bashrc with whatever edit you are comfortable with (nano or pico are good choices if you are not familiar with any) with the command:<br>
nano .bashrc<br>then add:<br>export PYTHONPATH=$PYTHONPATH:/home/omero_user/omero_path/lib/python/<br>to the file.<br><br>jmw<br><br><div class="gmail_quote">On Sat, Dec 12, 2009 at 5:15 AM, Gordon W. Laurie <span dir="ltr"><<a href="mailto:glaurie@virginia.edu" target="_blank">glaurie@virginia.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">We are having an apparent PYTHONPATH issue (see thread below) and have the suggestion from Ruben to edit our /home/@user/.bashrc file then add an export PYTHONPATH line.<br>
<br> Two questions:<br> 1. Having a limited working knowledge of Unix, how do we edit this file?<br> 2. Since we are running OMERO 4.0.3 and Python 2.5.1, should be first do upgrades on both, then work out problems later. Can we upgrade directly from OMERO 4.0.3 to 4.1.1?<br>
<br> Gordon.<br> <br> <br> <br> Begin forwarded message:<br> <br> From: Ruben Bernardo Alves <<a href="mailto:rubenalves@fm.ul.pt" target="_blank">rubenalves@fm.ul.pt</a>><br> Date: December 11, 2009 8:36:05 PM EST<br>
To: "Gordon W. Laurie" <<a href="mailto:glaurie@virginia.edu" target="_blank">glaurie@virginia.edu</a>><br> Subject: Re: [ome-users] ImportError: No module name Ice2<br> <br> I don't know, try to post this question on the OMERO forum.<br>
<br> Cheers<br> <br> -----"Gordon W. Laurie" <<a href="mailto:glaurie@virginia.edu" target="_blank">glaurie@virginia.edu</a>> wrote: -----<br> <br> To: » Ruben Alves <<a href="mailto:rubenalves@fm.ul.pt" target="_blank">rubenalves@fm.ul.pt</a>><br>
From: "Gordon W. Laurie" <<a href="mailto:glaurie@virginia.edu" target="_blank">glaurie@virginia.edu</a>><br> Date: 12/11/2009 08:05PM<br> Subject: Re: [ome-users] ImportError: No module name Ice2<br> <br>
Dear Ruben:<br> <br> I note that you are using Python2.6. Would it make sense to upgrade now to<br> the latest Python (Python 2.6.4), and to Omero 4.1.1? Then work out any<br> problems later. Can I go upgrade to the latter directly from 4.0.3?<br>
<br> Gordon.<br> <br> <br> <br> On Fri, 11 Dec 2009 10:20:17 +0000<br> » Ruben Alves <<a href="mailto:rubenalves@fm.ul.pt" target="_blank">rubenalves@fm.ul.pt</a>> wrote:<br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
OK, try to edit your /home/@user/.bashrc, and at the end add the following line:<br> export PYTHONPATH=/usr/lib/pymodules/python2.6/:/opt/Ice-3.3/python/:/@your_OMERO_path/lib/python/:/usr/local/lib/python2.6/:/usr/lib/python2.6/<br>
<br> There are severals path for python lib, I was able to run "something" only with long path.<br> <br> note: I'm running Omero 4.1.1<br> <br> Cheers<br> <br> <br> <br> <br> Gordon W. Laurie wrote:<br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks, I ran echo $PYTHONPATH and got '/opt/Ice-3.3/python:'. I assume this indicates an okay path. Below is the Python info.<br> <br> Gordon.<br> <br> Python 2.5.1 (r251:54863, Feb 6 2009, 19:02:12)<br> [GCC 4.0.1 (Apple Inc. build 5465)] on darwin<br>
<br> <br> <br> <br> On Thu, 10 Dec 2009 19:21:11 +0000<br> Ruben Bernardo Alves <<a href="mailto:rubenalves@fm.ul.pt" target="_blank">rubenalves@fm.ul.pt</a>> wrote:<br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Gordon,<br> Did you check your $PYTHONPATH ?<br> ex: echo $PYTHONPATH<br> <br> note: maybe a python update could break the links or the path.<br> <br> Cheers<br> <br> <br> -----<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@lists.openmicroscopy.org.uk</a> wrote: -----<br>
<br> To: <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br> From: "Gordon W. Laurie" <<a href="mailto:glaurie@virginia.edu" target="_blank">glaurie@virginia.edu</a>><br>
Sent by: <a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@lists.openmicroscopy.org.uk</a><br> Date: 12/10/2009 07:15PM<br> Subject: [ome-users] ImportError: No module name Ice<br>
<br> Upon restarting OMERO, I am encountering 'ImportError: No module named Ice'. Have OMERO 4.0.3 running and Ice 3.3.1.<br> <br> Any suggestions?<br> <br> Gordon.<br> <br> <br> <br> Gordon W. Laurie, PhD<br> Associate Professor<br>
Department of Cell Biology<br> Director, Biotechnology Training Program<br> University of Virginia<br> _______________________________________________<br> ome-users mailing list<br> <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br>
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</blockquote> <br> <br> Gordon W. Laurie, PhD<br> Associate Professor<br> Department of Cell Biology<br> Director, Biotechnology Training Program<br> University of Virginia<br> <br> </blockquote> <br> <br> -- <br> Ruben Alves System Analyst USI @ Instituto de Medicina Molecular<br>
Edifício Egas Moniz Av. Prof. Egas Moniz 1649-028 Lisboa Portugal tel: 217999411 ext 47026<br> <a href="mailto:rubenalves@fm.ul.pt" target="_blank">rubenalves@fm.ul.pt</a><br> <br> <br> </blockquote> <br> <br> <br> <br> Gordon W. Laurie, PhD<br>
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