Omero 4.2 server install on OS X 10.6.4

[graeme_b]

Hi,

I have been trying to install an Omero server, for the purpose of testing integration of image analysis scripts.

I tried following your 'Walkthrough on 10.6 using MacPorts', but I get stuck because the port for Ice 3.3.1 no longer installs (on trying to start the server with Ice 3.4, I get: IcePy Version is not compatible with ^3[.]3[.].*: 3.4.1).

Is there an easy way to install Ice 3.3.1.? (are you planning to move to the latest version at some point?) I tried following instructions I found on one of your threads here, but it failed to compile:

:info:build Instance.cpp: In member function 'void IceSSL::Instance::traceConnection(SSL*, bool)':
:info:build Instance.cpp:992: error: invalid conversion from 'const SSL_CIPHER*' to 'SSL_CIPHER*'

Thanks,

Graeme

[jmoore]

Hi Graeme,

is the post you found on the ZeroC site http://www.zeroc.com/forums/help-center/5069-make-error.html#post22222? If so, could you attach the full output of running

Code: Select all

sudo sh Mac64Build.sh

If you are on 10.6, we have pre-built binaries that we use internally. See https://www.glencoesoftware.com/mac/10.6/Ice-3.3.1-64.tar.bz2, and let us know how your mileage varies.

Cheers,
~Josh.

[graeme_b]

Hi,

thanks for that. I tried running Mac64Build.sh, and after changing:-

cp Make.rules.Darwin cpp/config/Make.rules.Darwin

to:-

cp Make.rules.Darwin /opt/local/var/macports/build/_Users_gball_build_OMERO.server-Beta-4.2.0_dports_devel_ice-cpp/work/Ice-3.3.1/cpp/config/Make.rules.Darwin

the script gets past "make -j $J install prefix=/opt/Ice-3.3.1-64 OPTIMIZE=yes", but then when it tries:-

make install prefix=/opt/Ice-3.3.1-64 OPTIMIZE=yes CXX="ccache g++"

it tries:-

ccache g++ -bundle -O2 -DNDEBUG -ftemplate-depth-128 -Wall -D_REENTRANT -L../../python -o ../../python/IcePy.so.3.3.1 Communicator.o Connection.o Current.o ImplicitContext.o Init.o Logger.o ObjectAdapter.o ObjectFactory.o Operation.o Properties.o Proxy.o Slice.o ThreadNotification.o Types.o Util.o -L../../../cpp/lib -lIce -lSlice -lIceUtil -F/opt/local/Library/Frameworks -framework Python

which gives me:-

ld: library not found for -lIce
collect2: ld returned 1 exit status
make[2]: *** [../../python/IcePy.so.3.3.1] Error 1
make[1]: *** [install] Error 1

Why can't it find libIce? Is it looking for libIce.dylib, which is in /opt/local/lib/ ? I tried setting DYLD_LIBRARY_PATH and LD_LIBRARY_PATH to /opt/local/lib, but that doesn't help. To be honest, I'm a bit out of my depth here - I'm not sure exactly what Mac64Build.sh is trying to do.

Any help much appreciated,

Cheers,

Graeme

[jmoore]

Hi Graeme,

the build script is attempting to build a standalone version of Ice (one to put under /opt). I didn't test how it would work with the MacPorts build, since there could be other modification made to those Makefiles. Could you try the pre-built binaries and let us know how it goes?

Thanks,
~J

[graeme_b]

Hi,

sorry, I think we have our wires crossed somehow - when you say "try the pre-built binaries", what do I actually need to do? When I unzip Ice-3.3.1-64.tar.bz2, I have a directory containing:-

-rw-r--r--@ 1 gball gball 346 3 Jun 21:11 HOW_TO
-rw-r--r--@ 1 gball gball 2908 3 Jun 21:11 HOW_TO.rules
-rw-r--r--@ 1 gball gball 1893 20 Mar 2009 ICE_LICENSE
-rw-r--r--@ 1 gball gball 18014 20 Mar 2009 LICENSE
drwx------@ 4 gball gball 136 11 Nov 16:57 Mac64Build
drwxr-xr-x@ 25 gball gball 850 3 Jun 21:06 bin
drwxr-xr-x@ 8 gball gball 272 3 Jun 20:12 config
drwxr-xr-x@ 13 gball gball 442 3 Jun 21:06 include
drwxr-xr-x@ 39 gball gball 1326 3 Jun 21:06 lib
drwxr-xr-x@ 112 gball gball 3808 14 Jun 17:42 python
drwxr-xr-x@ 9 gball gball 306 3 Jun 20:12 slice
-rw-r--r--@ 1 gball gball 4532599 30 Jul 09:08 tags

What I've tried so far, is to follow the HOW_TO instructions (and the Mac64Build.sh)

should I, rather, copy the contents of the bin/ and lib/ directories somewhere for instance?

Thanks,

Graeme

[jmoore]

Ah, sorry Graeme. There has been a misunderstanding. That directory although there are other bits and pieces is a complete Ice build. You should put it somewhere like /opt/Ice-3.3.1-64 and then add it your PATH PYTHONPATH and DYLD_LIBRARY_PATH environment variables:

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    export ICE_HOME=/opt/Ice-3.3.1-64
    export PATH=$ICE_HOME/bin:$PATH
    export DYLD_LIBRARY_PATH=$ICE_HOME/lib:$ICE_HOME/python:$DYLD_LIBRARY_PATH
    export PYTHONPATH=$ICE_HOME/python:$PYTHONPATH


Hope that helps!
~Josh.

[graeme_b]

Hi again,

after copying the directory to /opt/Ice-3.3.1-64 and updating the paths as you suggest, I tried running python and importing the Ice module to check which version python is using:-

bioch2122:OMERO.server-Beta-4.2.0 gball$ python
Python 2.6.6 (r266:84292, Oct 22 2010, 17:51:34)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import Ice
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/opt/Ice-3.3.1-64/python/Ice.py", line 19, in <module>
import IcePy
ImportError: dlopen(/opt/Ice-3.3.1-64/python/IcePy.so, 2): Symbol not found: _iconv
Referenced from: /opt/Ice-3.3.1-64/lib/libIce.33.dylib
Expected in: /opt/local/lib/libiconv.2.dylib
in /opt/Ice-3.3.1-64/lib/libIce.33.dylib

I installed libiconv with 'port', but still no joy I am currently updating all my ports to see if that helps - which version of libiconv do you have installed?

Regards,

Graeme

[jmoore]

Code: Select all

~ $ port installed | grep iconv
  libiconv @1.13.1_0
  libiconv @1.13.1_0+universal (active)


If that doesn't work, then we may be back to building directly on your system.

Good luck,
~Josh.

[graeme_b]

Hi,

currently, I get:-

port installed |grep libiconv
libiconv @1.11_4+darwin_8
libiconv @1.13.1_0 (active)

so perhaps my 'libiconv @1.13.1_0' is slightly different to your 'ibiconv @1.13.1_0+universal', but I guess that isn't an option for OS X?

I will either try to build using the tarball you sent me, or give up and try to find a linux box to install on instead.

Cheers,

Graeme

[jmoore]

To install libiconv with the universal flag use:

Code: Select all

sudo port install libiconv @universal


I don't know if that will solve your issue but it may be worth a try.
~Josh.