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>
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Hi Oscar,
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<div>sorry for the delay.</div>
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<div>On 6 Nov 2012, at 19:28, Oscar wrote:</div>
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<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>
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</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">
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<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 class="Apple-tab-span" style="white-space:pre"> </span>git<span class="Apple-tab-span" style="white-space:pre"> </span>mplayer<span class="Apple-tab-span" style="white-space:pre"> </span>python<span class="Apple-tab-span" style="white-space:pre"> </span>xz</div>
<div>ccache<span class="Apple-tab-span" style="white-space:pre"> </span>hdf5<span class="Apple-tab-span" style="white-space:pre"> </span>ossp-uuid<span class="Apple-tab-span" style="white-space:pre"> </span>readline<span class="Apple-tab-span" style="white-space:pre"> </span>yasm</div>
<div>gdbm<span class="Apple-tab-span" style="white-space:pre"> </span>jpeg<span class="Apple-tab-span" style="white-space:pre"> </span>pkg-config<span class="Apple-tab-span" style="white-space:pre"> </span>sqlite<span class="Apple-tab-span" style="white-space:pre"> </span>zeroc-ice33</div>
<div>gfortran<span class="Apple-tab-span" style="white-space:pre"> </span>mcpp<span class="Apple-tab-span" style="white-space:pre"> </span>postgresql<span class="Apple-tab-span" style="white-space:pre"> </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>
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<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>
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</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>
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<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>
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Sebastien</div>
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<div class="gmail_quote"><span><font color="#888888"><br>
~O </font></span></div>
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<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>
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The University of Dundee is a registered Scottish Charity, No: SC015096
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