Hi Sebastien,<div><br></div><div>I have cleaned up my path a little bit and moved /usr/local/bin to the front. Now it is as follows:</div><div>/usr/local/bin:/Library/Java/Home/bin:/Library/Java/Home/bin:/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/X11/bin</div>
<div><br></div><div>However the "you must brew install git" error didn't go away when I did "brew install omero".</div><div><br></div><div>Also I am confused when you say that I should remove paths related to ice from DYLD_LIBRARYPATH, because the official walkthrough I was following suggests doing the following:</div>
<div><pre style="overflow-x:auto;overflow-y:hidden;font-family:Consolas,'Deja Vu Sans Mono','Bitstream Vera Sans Mono',monospace;font-size:14.399999618530273px;line-height:16.799999237060547px;padding:0.5em;border:1px solid rgb(204,204,204);background-color:rgb(241,241,241);max-width:60em">
export BREW_DIR=$(brew --prefix)
export ICE_CONFIG=$(brew --prefix omero)/etc/ice.config
export ICE_HOME=$(brew --prefix zeroc-ice33)
export PYTHONPATH=$(brew --prefix omero)/lib/python:$ICE_HOME/python

export PATH=$BREW_DIR/bin:$BREW_DIR/sbin:/usr/local/lib/node_modules:$ICE_HOME/bin:$PATH
export DYLD_LIBRARY_PATH=$ICE_HOME/lib:$ICE_HOME/python:$DYLD_LIBRARY_PATH</pre></div><div><br></div><div>Should these environment variables set after brew install omero or before? In the walkthrough, the configuration comes after the omero installation step.</div>
<div><div><br></div><div>I have linked the python that was installed by brew in /usr/local/opt/zeroc-ice33/python. When I tried to import Ice, it crashed again (version mismatch).</div><div><br></div><div>Oscar</div><div>
<br></div><div><br></div><div><br></div><br><div class="gmail_quote">On Tue, Nov 13, 2012 at 10:06 AM, Sebastien Besson <span dir="ltr"><<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">



<div style="word-wrap:break-word">
Hi Oscar,
<div><br>
</div>
<div>looks like you need to clean your environment variables.</div>
<div><br>
</div>
<div>If you want to use your Homebrew Python, you want to </div>
<div>first `brew link python` and then put /usr/local/bin in front of </div>
<div>your PATH (this may also solve your "You must brew install git"  </div>
<div>issue).</div>
<div><br>
</div>
<div>Also you should remove paths to both ice 3.3 and ice 3.4 in your</div>
<div>DYLD_LIBRARYPATH and PATH.</div>
<div><br>
</div>
<div>Let me know if this helps moving forward,</div>
<div>Sebastien</div><div><div class="h5">
<div><br>
<div>
<div>On 13 Nov 2012, at 14:13, Oscar wrote:</div>
<br>
<blockquote type="cite">
<div>Content in my bashrc:</div>
<div>export PATH=$PATH:$JAVA_HOME/bin:$JRE_HOME/bin:$ICE_HOME/bin:$POSTGRES_HOME/bin:$PYTHONPATH/bin</div>
<div>export PYTHONPATH=/Library/Frameworks/Python.framework/Versions/2.7:$ICE_HOME/python</div>
<div>export ICE_HOME=/usr/local/opt/zeroc-ice33</div>
<div>export DYLD_LIBRARY_PATH=$ICE_HOME/lib:/$ICE_HOME/python:$DYLD_LIBRARY_PATH</div>
<div><br>
</div>
echo $PATH 
<div>/Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/X11/bin:/Users/oscar/bin:/Users/oscar/Downloads/iRODS/clients/icommands/bin:/Library/Java/Home/bin:/Library/Java/Home/bin:/usr/local/Ice-3.4.2/bin:/bin:/Users/oscar/bin:/Users/oscar/Downloads/iRODS/clients/icommands/bin:/Library/Java/Home/bin:/Library/Java/Home/bin:/usr/local/Ice-3.4.2/bin:/bin:/Library/Frameworks/Python.framework/Versions/2.7:/usr/local/Ice-3.4.2/python/bin:/Users/oscar/bin:/Library/Java/Home/bin:/Library/Java/Home/bin:/usr/local/opt/zeroc-ice33/bin:/bin:/Library/Frameworks/Python.framework/Versions/2.7:/usr/local/opt/zeroc-ice33/python/bin:/Users/oscar/bin:/Library/Java/Home/bin:/Library/Java/Home/bin:/usr/local/opt/zeroc-ice33/bin:/bin:/Library/Frameworks/Python.framework/Versions/2.7:/usr/local/opt/zeroc-ice33/python/bin</div>

<div><br>
</div>
<div>echo $PYTHONPATH</div>
<div>/Library/Frameworks/Python.framework/Versions/2.7:/usr/local/opt/zeroc-ice33/python</div>
<div><br>
</div>
<div>echo $DYLD_LIBRARY_PATH</div>
<div>/usr/local/opt/zeroc-ice33/<a>lib://usr/local/opt/zeroc-ice33/python:/usr/local/opt/zeroc-ice33/lib://usr/local/opt/zeroc-ice33/python::/usr/local/Ice-3.4.2/lib://usr/local/Ice-3.4.2/python::/usr/local/Ice-3.4.2/lib://usr/local/Ice-3.4.2/python::</a></div>

<div><br>
</div>
<div><br>
</div>
<div>It is weird that old Ice-3.4.2 path still there in PATH and DYLD_LIBRARY_PATH although I do have any thing like that in my bashrc. Does it look suspicious to you?</div>
<div><br>
</div>
<div>Oscar</div>
<div><br>
<br>
<div class="gmail_quote">On Tue, Nov 13, 2012 at 5:32 AM, Sebastien Besson <span dir="ltr">
<<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div>Forgot to mention PYTHONPATH as well</div>
<span><font color="#888888">
<div><br>
</div>
<div>Sebastien</div>
<div><br>
</div>
</font></span>
<div>
<div>
<div>On 12 Nov 2012, at 20:40, Oscar wrote:</div>
<br>
</div>
<div>
<div>
<blockquote type="cite">Hi Sebastien,
<div><br>
</div>
<div>Thanks for your reply. See the outputs of these commands below.
<div><br>
<div class="gmail_quote">On Mon, Nov 12, 2012 at 4:32 AM, Sebastien Besson <span dir="ltr">
<<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Oscar,
<div><br>
</div>
<div>sorry for the delay.</div>
<div><br>
<div>
<div>
<div>On 6 Nov 2012, at 19:28, Oscar wrote:</div>
<br>
<blockquote type="cite">
<div class="gmail_quote">Hi,<br>
<br>
I followed the walk through to install omero server 4.4 in Mac Lion<br>
using homebrew.<br>
(<a href="http://www.openmicroscopy.org/site/support/omero4/sysadmins/unix/server-install-homebrew.html" target="_blank">http://www.openmicroscopy.org/site/support/omero4/sysadmins/unix/server-install-homebrew.html</a>)<br>

All the steps up to ./omero_homebrew.sh are done. However when I was<br>
trying to install omero using "brew install omero", it says "you must<br>
brew install git". But git was already installed, because when I did<br>
"brew install git", it said "git-1.8.0 already installed". Since it<br>
doesn't let me install omero with brew, I had to install it manually.<br>
</div>
</blockquote>
<div><br>
</div>
</div>
<div>That is surprising indeed. Here are a couple of questions:</div>
<div>- where is brew installed i.e. what is the output of `which -a brew` and</div>
<div>`brew --prefix`?</div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>'which -a brew'  : /usr/local/bin/brew</div>
<div>'brew --prefix' : /usr/local</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div>
<div>
<div>- which packages are installed, i.e what is the output of `brew list`?</div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>'brew list' :</div>
<div>berkeley-db46<span style="white-space:pre-wrap"> </span>git<span style="white-space:pre-wrap">
</span>mplayer<span style="white-space:pre-wrap"> </span>python<span style="white-space:pre-wrap">
</span>xz</div>
<div>ccache<span style="white-space:pre-wrap"> </span>hdf5<span style="white-space:pre-wrap">
</span>ossp-uuid<span style="white-space:pre-wrap"> </span>readline<span style="white-space:pre-wrap">
</span>yasm</div>
<div>gdbm<span style="white-space:pre-wrap"> </span>jpeg<span style="white-space:pre-wrap">
</span>pkg-config<span style="white-space:pre-wrap"> </span>sqlite<span style="white-space:pre-wrap">
</span>zeroc-ice33</div>
<div>gfortran<span style="white-space:pre-wrap"> </span>mcpp<span style="white-space:pre-wrap">
</span>postgresql<span style="white-space:pre-wrap"> </span>szip </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div>
<div>
<div><br>
<blockquote type="cite">
<div class="gmail_quote">After I compiled Omero, I tried to run the executable "omero" under<br>
/dist/bin and python suddenly crashed "Fatal Python error: Interpreter<br>
not initialized (version mismatch?)". I installed python 2.7 with<br>
brew. It seemed this error has to do with Ice. I installed Ice 3.4 by<br>
just downloading the precompiled Ice3.4 tar ball from omero website,<br>
unzip it and add the environment variables accordingly including<br>
ICE_HOME, etc. I remember seeing it somewhere Ice 3.4 might not be<br>
compatible with OSX 10.7. Do I have to download Ice-3.3 instead? How<br>
do I fix this problem?<br>
</div>
</blockquote>
<div><br>
</div>
</div>
<div>Looks more like a pure Python issue here. What is the output of `<span style="font-family:monospace">which python` and</span></div>
<div><span style="font-family:monospace">`python -version` ? </span>And do you have the Homebrew Python in your PATH and</div>
<div>PYTHONPATH?</div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>I agree that my python is messed up. I installed python multiple times, including using brew install, and reinstalling Xcode. Now, the default python is the one that comes with Xcode "/Library/Frameworks/Python.framework/Versions/2.7/bin/python". I actually
 thought I should install python through brew this time. But when I did "brew install python" I got error "python-2.7.3 already installed, it's just not linked". Could python not linked be the problem that is causing the version mismatch error? How do I link
 python if it was installed with Xcode?</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div>
<div>
<div><br>
</div>
<div>Re Ice, if you followed the Homebrew walkthrough instructions, Ice 3.3 should have been</div>
<div>installed as part of the dependencies (`brew --prefix zeroc-ice33`). We  are still having </div>
<div>issues when installing OMERO with  Ice 3.4 using Homebrew. This is definitely on our todo list.</div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>I did not realize ice 3.3 was installed automatically by brew. Apparently, it was (indicated by 'brew list'). What I did earlier was download the pre-compiled Ice-3.4.2 or Ice-3.3.1 and move the directory to /usr/local. So I changed ICE_HOME to '/usr/local/opt/zeroc-ice33'
 and PYTHONPATH accordingly and compiled omero again. However I still got the "interpreter not initialized" error. I got the same error when I did "import Ice" from python too. Also I tried to install omero with brew and it still asked to brew install git first.
 Interestingly, I did "brew install omero43" and it was actually trying to download the tarball instead of complaining about git although the downloading stuck at 0.0% the whole time.</div>
<div><br>
</div>
<div><br>
</div>
<div>Do you have any idea what is still messed up here? Should I reinstall everything from the beginning again? How do I clean up everything that was installed by brew?</div>
<div><br>
</div>
<div>Thanks</div>
<div><br>
</div>
<div>Oscar</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div>
<div>
<div><br>
</div>
Sebastien</div>
<div><br>
<blockquote type="cite">
<div class="gmail_quote"><span><font color="#888888"><br>
~O </font></span></div>
<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>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
</blockquote>
</div>
<br>
<div>
<div style="word-wrap:break-word"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:medium;white-space:normal;font-family:Helvetica;word-spacing:0px">
<div style="word-wrap:break-word">
<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK   Tel: (01382) 386364</div>
</div>
</span></div>
</div>
<br>
</div>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096 </div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
</div>
</div>
</div>
<div>
<div><br>
<div><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:medium;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:medium;white-space:normal;font-family:Helvetica;word-spacing:0px">
<div style="word-wrap:break-word"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:medium;white-space:normal;font-family:Helvetica;word-spacing:0px">
<div style="word-wrap:break-word">
<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK   Tel: (01382) 386364</div>
</div>
</span></div>
</span></span></div>
<br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096 </div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</blockquote>
</div>
<br>
<div><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:medium;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:medium;white-space:normal;font-family:Helvetica;word-spacing:0px">
<div style="word-wrap:break-word"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:medium;white-space:normal;font-family:Helvetica;word-spacing:0px">
<div style="word-wrap:break-word">
<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK   Tel: (01382) 386364</div>
</div>
</span></div>
</span></span></div>
<br>
</div>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096
</div></div></div>

</blockquote></div><br></div>