[ome-users] omero installation error

Josh Moore josh at glencoesoftware.com
Fri Sep 21 20:23:13 BST 2012 

On Sep 21, 2012, at 9:10 PM, Oscar wrote:

> So I tried to reinstall ice with homebrew this time after clearing up any
> OME related environment variables in my source file. All the ice dependency
> packages installed ok including db and mcpp. However, got hundreds of error
> while compiling Ice 3.4 starting with the following:
> c++ -c -I.. -I../../include -DICE_API_EXPORTS   -O2 -DNDEBUG -Wall
> -D_REENTRANT Direct.cpp
> In file included from Current.cpp:24:
> In file included from ../../include/Ice/Current.h:24:
> In file included from ../../include/Ice/LocalObjectF.h:15:
> ../../include/Ice/Handle.h:106:13: error: call to function 'upCast' that is
> neither visible in the template definition nor found by argument-dependent
> lookup
>            upCast(this->_ptr)->__decRef();
>            ^
> 
> Do you know what's causing it? Is there any other way to install Ice 3.4.
> The omero website indicates that omero 3.3 would not work my Mac Lion, so
> that is not an option.

The default homebrew formula for ice won't work on 10.7, but we do have a version that will. The upcoming release (4.4.4) contains an updated walk-through that explains this. To save yourself any more troubles, you might take a look at:

   https://www.openmicroscopy.org/site/support/omero4-staging/sysadmins/unix/server-install-homebrew.html

but keep in mind that the "-staging" will be dropped from that URL for the release version.

Hope this helps you have a better weekend! :)

Cheers,
~Josh.


> On Fri, Sep 21, 2012 at 1:39 PM, Josh Moore <josh at glencoesoftware.com>wrote:
> 
>> Hi Oscar,
>> 
>> On Sep 21, 2012, at 8:34 PM, Oscar wrote:
>> 
>>> I added the following lines in my bashrc according to the README of
>> Ice3.4.1
>>> export ICE_HOME=/usr/share/Ice-3.4.1
>>> export PYTHONPATH=/usr/lib/python2.7:$ICE_HOME/python
>>> export
>> DYLD_LIBRARY_PATH=/usr/share/java:/usr/lib/:/usr/share/Ice-3.4.1:$DYLD_LIBRARY_PATH
>>> export
>> CLASSPATH=$ICE_HOME/lib/Ice.jar:$ICE_HOME/lib/Freeze.jar:$ICE_HOME/lib/db.jar:$CLASSPATH
>>> export
>> PATH=$PATH:$JAVA_HOME/bin:$JRE_HOME/bin:$ICE_HOME/bin:$POSTGRES_HOME/bin
>>> #ant -Dice.home=$ICE_HOME
>> 
>> At this point, is "slice2java --version" returning "3.4.1"?
>> 
>> 
>>> Still got the same error. (pasted below again):
>>> ==> ./build.py -Dice.home=/usr/local build-default
>>> Error getting version for BUILD_NUMBER=
>>> Result: 133
>>> 
>>> BUILD FAILED
>>> /private/tmp/brew-omero-4.4.1-sPcQ/build.xml:36: The following error
>>> occurred while executing this line:
>>> 
>> /private/tmp/brew-omero-4.4.1-sPcQ/components/antlib/resources/global.xml:310:
>>> Cannot find slice2java!
>>> 
>>> 
>> *******************************************************
>>>                   Ice is not properly installed. Cannot find slice2java
>>> 
>> *******************************************************
>>> 
>>> Total time: 0 seconds
>>> 
>>> Looks like the ice.home wasn't set right, /usr/local isn't where Ice is
>>> installed. Note the last line in my environment file which I commented
>> out.
>>> It is in the README file, but it gives me error if I have it in there.
>> Does
>>> it have to do with the error? How do I set ice.home correctly in my
>> bashrc.
>>> Also, Ice Readme says either ice.home or ICE_HOME works, but it seems
>>> ICE_HOME has been  ignored by homebrew the whole time, even though it is
>>> set in bashrc
>> 
>> There are several things that we're trying to workout at once. My
>> assumption is that if you have slice2java working, then the omero build
>> (./build.py) should complete. If not, you may have to install Ice via
>> homebrew in which case ice.home/ICE_HOME would in fact be under /usr/local.
>> 
>> Cheers,
>> ~Josh.
>> 
>> 
>>> On Fri, Sep 21, 2012 at 9:25 AM, Josh Moore <josh at glencoesoftware.com
>>> wrote:
>>> 
>>>> 
>>>> On Sep 21, 2012, at 4:17 PM, Oscar wrote:
>>>> 
>>>>> I did the exact command `brew --prefix ice`/bin/slicejava --version, it
>>>>> said: -bash: /usr/local/Cellar/ice/3.4.2/bin/slicejava: No such file or
>>>>> directory
>>>>> 
>>>>> I do not understand why it points to Cellar while Ice is installed
>> under
>>>>> /usr/share/Ice-3.4.1 by default.
>>>>> 
>>>>> Then I tried "/usr/share/Ice-3.4.1/bin/slice2java --version" still
>>>> nothing,
>>>>> but gave me this error:
>>>>> 
>>>>> dyld: Library not loaded: /opt/Ice-3.4/lib/libSlice.34.dylib
>>>>> Referenced from: /usr/share/Ice-3.4.1/bin/slice2java
>>>>> Reason: image not found
>>>>> Trace/BPT trap: 5
>>>> 
>>>> Ah, ok. If you've installed Ice under /usr/share/Ice-3.4.1 (which
>> doesn't
>>>> belong to homebrew), then you'll need to set PATH and DYLD_LIBRARY_PATH
>> to
>>>> point at bin and lib, respectively, to get Ice running. This is what is
>>>> described in the README under Ice-3.4.1.
>>>> 
>>>> Cheers,
>>>> ~Josh.
>>>> 
>>>> 
>>>>> On Fri, Sep 21, 2012 at 9:11 AM, Josh Moore <josh at glencoesoftware.com
>>>>> wrote:
>>>>> 
>>>>>> 
>>>>>> On Sep 21, 2012, at 4:08 PM, Oscar wrote:
>>>>>> 
>>>>>>> slice2java --version (-version, -v) or even man slice2java gave me
>>>>>> nothing,
>>>>>>> but it came with Ice-3.4 if that helps.
>>>>>> 
>>>>>> So until "slice2java --version" works properly the OMERO build can
>>>>>> definitely not complete. What's on your $PATH?  Does `brew --prefix
>>>>>> ice`/bin/slicejava --version  return anything?
>>>>>> 
>>>>>> Cheers,
>>>>>> ~Josh
>>>>>> 
>>>>>> 
>>>>>>> The link for the walk-thru is:
>>>>>>> 
>>>>>> 
>>>> 
>> http://www.openmicroscopy.org/site/support/omero4/server/install-walkthrough-on-10.7-using-homebrew
>>>>>>> 
>>>>>>> Thanks
>>>>>>> 
>>>>>>> On Fri, Sep 21, 2012 at 2:54 AM, Josh Moore <
>> josh at glencoesoftware.com
>>>>>>> wrote:
>>>>>>> 
>>>>>>>> Hi Oscar,
>>>>>>>> 
>>>>>>>> On Sep 20, 2012, at 11:40 PM, Oscar wrote:
>>>>>>>> 
>>>>>>>>> I was following the walkthrough of installing Omero with Homebrew
>> on
>>>>>> Mac
>>>>>>>>> Lion and got stuck at the "brew install omero" step. Got the
>>>> following
>>>>>>>>> error:
>>>>>>>> 
>>>>>>>> Can you post the link to the walk-through you're using just to make
>>>> sure
>>>>>>>> we're looking at the same version?
>>>>>>>> 
>>>>>>>>> ==> ./build.py -Dice.home=/usr/local build-default
>>>>>>>>> Error getting version for BUILD_NUMBER=
>>>>>>>>> Result: 133
>>>>>>>>> 
>>>>>>>>> BUILD FAILED
>>>>>>>>> /private/tmp/brew-omero-4.4.1-gxMx/build.xml:36: The following
>> error
>>>>>>>>> occurred while executing this line:
>>>>>>>>> 
>>>>>>>> 
>>>>>> 
>>>> 
>> /private/tmp/brew-omero-4.4.1-gxMx/components/antlib/resources/global.xml:310:
>>>>>>>>> Cannot find slice2java!
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>> *******************************************************
>>>>>>>>>                Ice is not properly installed. Cannot find
>>>> slice2java
>>>>>>>>> 
>>>>>>>> *******************************************************
>>>>>>>>> 
>>>>>>>>> I did a google search on this matter and found that similar
>> question
>>>>>> has
>>>>>>>>> been asked in the past. It could be resolved by creating a softlink
>>>> of
>>>>>>>>> slice2java from Ice3.4 directory to /usr/local/bin. Did that but
>>>> still
>>>>>>>> got
>>>>>>>>> the same error. Any suggestions?
>>>>>>>> 
>>>>>>>> 
>>>>>>>> What do `slice2java --version` and `which slice2java` say?
>>>>>>>> 
>>>>>>>> Cheers,
>>>>>>>> ~Josh.
>>>>>>>> 
>>>>>>>> 
>>>>>> 
>>>>>> 
>>>> 
>>>> 
>> 
>>

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