when I click "start OMERO insight" in the OMERO Reader node, KNIME crashes entirely (see below whats printed into the terminal).
I am running Knime 3.1.2 on linux mint 17.3.
If it helps I'd glady provide the error report file that is mentioned below.
Thanks for your help!
# A fatal error has been detected by the Java Runtime Environment:
# SIGSEGV (0xb) at pc=0x00007fbaab201eaf, pid=2663, tid=140439585056512
# JRE version: Java(TM) SE Runtime Environment (8.0_60-b27) (build 1.8.0_60-b27)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.60-b23 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C [libgdk-x11-2.0.so.0+0x4ceaf] gdk_display_open+0x3f
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
# An error report file with more information is saved as:
# If you would like to submit a bug report, please visit:
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
sorry for the trouble and thanks for letting us know. We will try to reproduce the problem and come back with a solution asap.
PS: Which OMERO Version are you using on the Server side? Just out of curiosity and to make sure that KNIME can connect.
PPS: We are working on a more flexible solution (based on imagej) to read/write images from and to OMERO.
thanks for the quick reply!
we are currently using OMERO 5.1.2 but are also in the process of upgrading to a more recent version.
Thanks for your help and cheers,
I was able to reproduce the problem. No I will work on a fix. ;-)
Thanks again for reporting,
I opened an issue in our GitHub Repo. We will tackle the problem next week.
thanks for the update! I'll stay tuned for next week then :)
many thanks for the feedback and the issue tracker link!
Hi Niko & Kai,
we fixed the Client for OMERO 5.2.x (available via our nightly build). We will also provide a version for OMERO 5.1.x (probably only via nightly build, hopefully next week).
However, as mentoined above, we want to redesign our OMERO integration and offer a new Reader/Writer based on imagej-omero / scifio. It would be great, as we don't have too much experience with OMERO, if you could provide us some feedback what are "must haves" and/or "nice-to-haves" of such new nodes (e.g. you want to read a complete dataset and then write back the results, or ...). We opened a GitHub issue for further discussion:
I hope this helps,