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

Tue Nov 13 14:13:28 GMT 2012

Content in my bashrc:
export
PATH=$PATH:$JAVA_HOME/bin:$JRE_HOME/bin:$ICE_HOME/bin:$POSTGRES_HOME/bin:$PYTHONPATH/bin
export
PYTHONPATH=/Library/Frameworks/Python.framework/Versions/2.7:$ICE_HOME/python
export ICE_HOME=/usr/local/opt/zeroc-ice33
export DYLD_LIBRARY_PATH=$ICE_HOME/lib:/$ICE_HOME/python:$DYLD_LIBRARY_PATH

echo $PATH
/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

echo $PYTHONPATH
/Library/Frameworks/Python.framework/Versions/2.7:/usr/local/opt/zeroc-ice33/python

echo $DYLD_LIBRARY_PATH
/usr/local/opt/zeroc-ice33/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::

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?

Oscar

On Tue, Nov 13, 2012 at 5:32 AM, Sebastien Besson <s.besson at dundee.ac.uk>wrote:

>  Forgot to mention PYTHONPATH as well
>
>  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>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
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>>   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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