Known Limitations

Software limitations

ValueError: filedescriptor out of range in select() when increasing the number of available filehandles via 'ulimit -n'

This is a known issue in Python versions prior to 2.7.0. See #6201 and Python Issue #3392 for more details.

Dv from OMX files (.hdr) files not viewable

Some files generated by an OMX system have a pixel type of float and a large dynamic range. While the files import into OMERO they are currently now viewable. This fix would require deep changes to several parts of the code and we have chosen not to make the changes yet. See #3256

Postgres 9.x defaults to 'hex' bytea_output format

Newer version of Postgres default to the 'hex' as opposed to 'escape' format for bytea_output which OMERO uses for storing script and share data in the DB. A workaround is available under "OMERO and PostgreSQL. See #5662

now() in Postgres functions show time of db upgrade/install

now() in Postgres functions show time of db upgrade/install. See #5862

Switching between 'Shares' in web

Occasionally you may find that when switching from a 'share' login on the webclient back to your own user login, you get an error saying that you don't have permission to access your data. This is a mix-up between the different 'sessions' and can be resolved with a simple log-out and log-in.

OMERO.web 'development server' does not work under Windows XP

The development server included with OMERO.web does not work under Windows XP. This server is included to allow you to easily evaluate and develop the OMERO.web component. As it should not be used in a production environment, while an inconvenience, this should not stop the deployment of a production version of OMERO.web. See OME forum topic

OMERO.importer and number of files to import

It is preferable not to import more than 1000 image files in a single import.

OMERO.importer on Ubuntu

Under older Ubuntu installations the 'import folder' option currently does not work.

Comment annotations and OMERO.clients

If you wish to add a large comment to an object (e.g. an Image), it is preferable to attach a file i.e. use FileAnnotation.

OMERO.insight History Feature

History feature in Viewer has been turned off since version 4.0.

OMERO.insight and Changing Group Permissions

Changing of group permissions for very large groups can be very slow #2874.

OMERO.insight and Moving Data

Data created/imported in a group cannot be moved to another group even if the user is a member of the 2 groups #3532.

Not finding certain pieces of data in wildcard searches

Sometimes data is missed when certain types of wildcard searches are performed. You can find further details on #3164.

C++ compilation problems on Mac OS X 10.6 (Snow Leopard)

Under certain circumstances building OmeroCpp on Mac OS X 10.6 (Snow Leopard) can fail with "ld: symbol(s) not found". You can find further details, a potential solution and make any comments on your experience with the problem on #3210.

Non-LDAP user password security

Encrypted login and communication, via SSL, has been available in OMERO for some time. However, under some circumstances it is possible for passwords to end up on the wire in the clear. Further details and status can be found on ticket #3232. Users who have their credentials stored in LDAP and who have OMERO configured to use their LDAP server are not affected by this issue.

Synchronising with LDAP

Enabling synchronisation of LDAP on user login will result in LDAP being treated as the authority on both group membership and also the available groups. Any groups defined in OMERO and not in LDAP will result in users being removed from these groups. The groups will still exist in OMERO but user membership will be treated as being defined by LDAP alone.

Moving data between groups

In 4.2.0 we expanded the support for collaborative work using OMERO, this is detailed on the permissions page. When any data is imported it is currently assigned a group and currently that decision is final. This will change with future releases but we encourage users to be aware of their working group at all times, especially when importing, see #3532.

Synchronization of lib/scripts

As described under OMERO.scripts, 4.2.0 includes a significantly improved scripting system. Several official scripts are shipped under lib/scripts in the deployment directory. If any of your users add their own "official scripts", they too will be stored under lib/scripts. When we release a new OMERO version, there will be some difficulties merging the two directories. We will address this issue as quickly as possible.

Import of reagents and screens

The import of some, complicated OME-XML files may not work with 4.2.0. Shortly before release, we tested a file with two entire screens, several plates, and many cross linked reagents which failed. This is a very unlikely scenario, and we know of no files that contain this level of data, but if you have issues getting screening data imported in the OME-XML format, please let us know.

Limited support for PostgreSQL 8.1

In order to reduce sporadic hangs, the 4.2 database introduced the use of the "pg_advisory_lock" method. This is not available on PostgreSQL 8.1, however. During db creation or upgraded the following message is printed:

        =====================================================================================
        pg_advisory_lock does not exist!

        You should consider upgrading to PostgreSQL 8.2 or above
        Until then, you may experience infrequent key constraint issues on insert.
        =====================================================================================

OMERO should continue to function normally, but in some cases an insert may throw an exception if two threads try to insert the same primary key.

Binary delete on Windows servers

On Windows servers not all binary files corresponding to a delete may be removed from the binary repository. See Delete: Binary Data for more details.