[ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5

Tue Aug 4 18:15:25 BST 2015

It looks like Debian 6 has the very old zeroc-ice33 in it's repos. Is this your own server, or was it setup by someone else? If OMERO was previously running then ice may have been installed in a non-standard location, which means you'll need to setup some environment variables e.g. PATH, PYTHONPATH.

Simon

On 4 August 2015 at 18:11, Jean-Marc Champagne <jean-marc.champagne at mhi-rc.org<mailto:jean-marc.champagne at mhi-rc.org>> wrote:
It’s installed on Debian 6
Linux version 3.2.0-4-amd64 (debian-kernel at lists.debian.org<mailto:debian-kernel at lists.debian.org>) (gcc version 4.6.3 (Debian 4.6.3-14) ) #1 SMP Debian 3.2.54-2

omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$ icegridnode --version
-bash: icegridnode: command not found

omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$ python -c 'import Ice; print Ice.stringVersion()'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named Ice

Thanks for the quick reply

JMarc

From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>] On Behalf Of Simon Li
Sent: 4 août 2015 13:03
To: OME User Support List

Subject: Re: [ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5

Hi Jean-Marc
What operating system are you using (including the full version)? The ice poackage might have a different name.
Can you run the following two commands in a console and paste the output?

icegridnode --version

python -c 'import Ice; print Ice.stringVersion()'
Thanks, Simon

On 4 August 2015 at 17:38, Jean-Marc Champagne <jean-marc.champagne at mhi-rc.org<mailto:jean-marc.champagne at mhi-rc.org>> wrote:
I re-installed it using Omero.server-5.1.2-ice34-b45 file downloaded from the Omero web site
[cid:image001.png at 01D0CEB6.A9E8A430]

And here’s the error msg I get
[cid:image002.png at 01D0CEB6.A9E8A430]

[cid:image004.png at 01D0CEB6.A9E8A430]

I verified if Ice was installed to find out it was not using
dpkg -s zeroc-ice34
dpkg-query: package 'zeroc-ice34' is not installed and no information is available
Use dpkg --info (= dpkg-deb --info) to examine archive files,
and dpkg --contents (= dpkg-deb --contents) to list their contents.

I went to the community and Maria had the same problem which she use to fix the probleme… what is the long line she is refering to ?

[cid:image005.png at 01D0CEB6.A9E8A430]
JMarc

From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>] On Behalf Of Sebastien Besson (Staff)
Sent: 1 août 2015 08:15
To: users OME
Subject: Re: [ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5

Hi Jean-Marc,

as we already suggested in the previous thread [1] [2], if you have Ice 3.4
installed via your package manager, could you try downloading the Ice 3.4
server and retry to start the server?
The upgrade of your version of Ice depends on your Linux distribution. More
information is available on the Ice 3.5 downloads page [3].

Best,
Sebastien

[1] http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-July/005508.html
[2] http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-July/005509.html
[3] https://zeroc.com/download_3_5_1.html

On 31 Jul 2015, at 15:18, Jean-Marc Champagne <jean-marc.champagne at mhi-rc.org<mailto:jean-marc.champagne at mhi-rc.org>> wrote:

I ran http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/server-upgrade.html#omero-web-configuration procedures, and had to upgrade postgres from 9.1 to 9.4 to be able to set it up.

psql -h localhost -U db_omero_usr omero_database < sql/psql/OMERO5.1__1/OMERO5.0__0.sql -p 5433

UPDATE 1
                               status
---------------------------------------------------------------------
                                                                    +
                                                                    +
                                                                    +
YOU HAVE SUCCESSFULLY UPGRADED YOUR DATABASE TO VERSION OMERO5.1__1+
                                                                    +
                                                                    +

(1 row)

COMMIT

Reindex was fine and so was the vacuum analyse

But when started omero, I received this error

How do I upgrade ICE ?
Any help would be greatly appreciated…

postgres at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$<mailto:postgres at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$> bin/omero admin start
Traceback (most recent call last):
  File "bin/omero", line 97, in <module>
    import omero.cli
  File "/home/OMS/apps/OMERO/OMERO.server-5.1.2-ice35-b45/lib/python/omero/__init__.py", line 43, in <module>
    raise Exception(msg)
Exception:

        ERROR: Ice version mismatch!

        Your OMERO code has been compiled using Ice version 3.5.1
        but you seem to have Ice version 3.4.2 installed. If you need
        help understanding this issue, please send this error message
        to the OME community:

        http://www.openmicroscopy.org/site/community

        Debugging Info:
        --------------
        VERSION=5.1.2-ice35-b45
        PYTHONPATH=/home/OMS/apps/OMERO/OMERO.server-5.1.2-ice35-b45/lib/python:/home/OMS/apps/OMERO/OMERO.server-5.1.2-ice35-b45/var/lib:/home/OMS/apps/OMERO/OMERO.server-5.1.2-ice35-b45/bin:/usr/lib/pymodules/python2.7:/home/OMS/apps/OMERO/OMERO.server-5.1.2-ice35-b45:/usr/lib/python2.7:/usr/lib/python2.7/plat-linux2:/usr/lib/python2.7/lib-tk:/usr/lib/python2.7/lib-old:/usr/lib/python2.7/lib-dynload:/usr/local/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages/PIL:/usr/lib/python2.7/dist-packages/gtk-2.0:/home/OMS/apps/OMERO/OMERO.server-5.1.2-ice35-b45/lib/fallback

JMarc
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The University of Dundee is a registered Scottish Charity, No: SC015096

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