[ome-users] omero server 4.4 installation problem on mac OSX 10.7.5

[Sebastien Besson]

Hi Oscar,

can you give you the content of your PATH and your DYLD_LIBRARY_PATH?

Sebastien

On 12 Nov 2012, at 20:40, Oscar wrote:

Hi Sebastien,

Thanks for your reply. See the outputs of these commands below.

On Mon, Nov 12, 2012 at 4:32 AM, Sebastien Besson <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>> wrote:
Hi Oscar,

sorry for the delay.

On 6 Nov 2012, at 19:28, Oscar wrote:

Hi,

I followed the walk through to install omero server 4.4 in Mac Lion
using homebrew.
(http://www.openmicroscopy.org/site/support/omero4/sysadmins/unix/server-install-homebrew.html)
All the steps up to ./omero_homebrew.sh are done. However when I was
trying to install omero using "brew install omero", it says "you must
brew install git". But git was already installed, because when I did
"brew install git", it said "git-1.8.0 already installed". Since it
doesn't let me install omero with brew, I had to install it manually.

That is surprising indeed. Here are a couple of questions:
- where is brew installed i.e. what is the output of `which -a brew` and
`brew --prefix`?

'which -a brew'  : /usr/local/bin/brew
'brew --prefix' : /usr/local

- which packages are installed, i.e what is the output of `brew list`?

'brew list' :
berkeley-db46 git mplayer python xz
ccache hdf5 ossp-uuid readline yasm
gdbm jpeg pkg-config sqlite zeroc-ice33
gfortran mcpp postgresql szip

After I compiled Omero, I tried to run the executable "omero" under
/dist/bin and python suddenly crashed "Fatal Python error: Interpreter
not initialized (version mismatch?)". I installed python 2.7 with
brew. It seemed this error has to do with Ice. I installed Ice 3.4 by
just downloading the precompiled Ice3.4 tar ball from omero website,
unzip it and add the environment variables accordingly including
ICE_HOME, etc. I remember seeing it somewhere Ice 3.4 might not be
compatible with OSX 10.7. Do I have to download Ice-3.3 instead? How
do I fix this problem?

Looks more like a pure Python issue here. What is the output of `which python` and
`python -version` ? And do you have the Homebrew Python in your PATH and
PYTHONPATH?

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?

Re Ice, if you followed the Homebrew walkthrough instructions, Ice 3.3 should have been
installed as part of the dependencies (`brew --prefix zeroc-ice33`). We  are still having
issues when installing OMERO with  Ice 3.4 using Homebrew. This is definitely on our todo list.

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.


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?

Thanks

Oscar

Sebastien


~O

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Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364


The University of Dundee is a registered Scottish Charity, No: SC015096


Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364


The University of Dundee is a registered Scottish Charity, No: SC015096
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