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

Thu Nov 15 12:27:23 GMT 2012

Hi Oscar,

On 14 Nov 2012, at 17:31, Oscar wrote:

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".

OK, git may be installed then not properly linked then. Can you run `brew link git`?
And show me the output of `brew info git`?

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.

They shouldn't be needed for the OMERO installation per se.  For instance
https://github.com/openmicroscopy/openmicroscopy/blob/develop/docs/hudson/OMERO-homebrew-install.sh
shows the list of steps we use to regularly test the Homebrew installation.

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).

How did you install Ice-3.3? Looks like this is not the Homebrew installed zeroc-ice33.
Which binaries did you use? Did you just put them in /usr/local or are there additional
steps?

Sebastien

Oscar

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

_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto: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

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20121115/5d06621b/attachment.html>