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

Wed Nov 14 17:31:11 GMT 2012

Hi Sebastien,

I have cleaned up my path a little bit and moved /usr/local/bin to the
front. Now it is as follows:
/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

However the "you must brew install git" error didn't go away when I did
"brew install omero".

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:

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

Should these environment variables set after brew install omero or before?
In the walkthrough, the configuration comes after the omero installation
step.

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).

Oscar

On Tue, Nov 13, 2012 at 10:06 AM, Sebastien Besson <s.besson at dundee.ac.uk>wrote:

>  Hi Oscar,
>
>  looks like you need to clean your environment variables.
>
>  If you want to use your Homebrew Python, you want to
> first `brew link python` and then put /usr/local/bin in front of
> your PATH (this may also solve your "You must brew install git"
> issue).
>
>  Also you should remove paths to both ice 3.3 and ice 3.4 in your
> DYLD_LIBRARYPATH and PATH.
>
>  Let me know if this helps moving forward,
> Sebastien
>
>  On 13 Nov 2012, at 14:13, Oscar wrote:
>
>  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
>>
>
>
>   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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