Cytoscape 3.6.1 crashes while selecting a protein

[akbi...@gmail.com]

Hi Scooter!

My Cytoscape V 3.6.1 crashes almost once every ten minute. I have save my work every 1-2 minute since I think that it may hang any time. This happens particularly when I select a protein molecule to either move it or see its property. Additionally, the right click menu also doesn't appear in general. However, if I add a new network, then the right click menu becomes active again. While starting Cytoscape, I see many of the apps don't load properly and Cytoscape shows error for those. I had Java 8 and JDK 10 loaded in my PC but I have also removed JDK10 to make sure that my Java environment is perfect for Cytoscape. In fact, I removed both versions and re-installed JAVA8. Then I uninstalled and re-installed Cytoscape 3.6.1. I have updated all apps in Cytoscape but still I have this issue. Please help!

[akbi...@gmail.com]

I have updated Cytoscape to V3.7.0 and Java to 8.191. But still many of the programs show error in loading and throw error: couldn't find resource .... The Cytoscape does hang. Please help!

[David Otasek]

Hello,

Some additional information would be helpful.

If you run the System Checker script located at https://cytoscape.org/troubleshooting.html, the information it produces will be very helpful, and should be posted here.

If Cytoscape is crashing during operation, it is also possible that you are running out of memory. If you click on the memory button in the lower right hand side of the Cytoscape window, it should show you if this is the case.

[akbi...@gmail.com]

Hi David,

My system seems to be fine. Please see the System Checker report below:

#################
Cytoscape System Requirements Checker for Windows
-------------------------------------------------

Target Cytoscape version: 3.7.0


Your Windows version is:

Microsoft Windows [Version 10.0.17134.376]

Java is installed

Your system is 64 bit

JAVA_HOME is not set

Your Java version is at least version 8 as required

Your Java version is no higher than version 8 as required

Your Java is 64 bit as recommended

The "app" store at apps.cytoscape.org is reachable



Summary
-------

Success! You are ready to run Cytoscape 3.7.0



More details on Java
--------------------

java version "1.8.0_191"
Java(TM) SE Runtime Environment (build 1.8.0_191-b12)
Java HotSpot(TM) 64-Bit Server VM (build 25.191-b12, mixed mode)



More details on apps.cytoscape.org
----------------------------------

Going to run trace route command for apps.cytoscape.org with timeout of 30000ms now...

Tracing route to apps.cytoscape.org [132.239.8.177]
over a maximum of 30 hops:

1 5 ms 3 ms 4 ms wifi-m-v880.net.unc.edu [152.23.8.3]
2 4 ms 5 ms 3 ms core-m-v1551.net.unc.edu [152.19.253.58]
3 6 ms 4 ms 4 ms border-m-v1214.net.unc.edu [152.19.255.65]
4 5 ms 5 ms 4 ms rtp-gw-to-uncmanning.ncren.net [128.109.19.89]
5 7 ms 8 ms 8 ms hntvl-ip-asr-gw-to-rtp-gw.ncren.net [128.109.9.6]
6 11 ms 8 ms 9 ms et-7-0-0.612.rtsw.char.net.internet2.edu [198.71.46.169]
7 14 ms 12 ms 13 ms et-4-1-0.4079.rtsw.atla.net.internet2.edu [162.252.70.124]
8 27 ms 29 ms 29 ms et-7-0-0.4079.rtsw.jcsn.net.internet2.edu [162.252.70.47]
9 36 ms 39 ms 39 ms et-8-3-0.4079.rtsw.houh.net.internet2.edu [162.252.70.44]
10 53 ms 52 ms 51 ms et-4-0-0.4079.rtsw.elpa.net.internet2.edu [162.252.70.14]
11 57 ms 58 ms 56 ms et-7-0-0.4079.rtsw.tucs.net.internet2.edu [162.252.70.21]
12 58 ms 57 ms 60 ms et-4-0-0.4079.rtsw.phoe.net.internet2.edu [162.252.70.22]
13 69 ms 67 ms 68 ms et-7-1-0.4079.rtsw.losa.net.internet2.edu [162.252.70.24]
14 68 ms 68 ms 68 ms hpr-lax-hpr2--i2-r&e.cenic.net [137.164.26.200]
15 70 ms 71 ms 70 ms hpr-ucsd-40ge-2--lax-hpr.cenic.net [137.164.26.30]
16 71 ms 90 ms 70 ms nodem-core-6807-vlan2761-gw.ucsd.edu [132.239.254.163]
17 69 ms 70 ms 120 ms agg-b-mcore.ucsd.edu [132.239.254.44]
18 71 ms 78 ms 78 ms cytoscape-apps.ucsd.edu [132.239.8.177]

Trace complete.



Press any key to continue . . .

###############

Also I have 16 GB of RAM and I have looked at it before. I don't run out of memory.

Any other suggestions?

Thanks in advance!
Akshaya

[akbi...@gmail.com]

Any suggestion how to bring back right mouse menu?

[David Otasek]

I wonder if this could be related to some of the apps you have installed. Could you give us a list of the installed apps?

It would also help to run cytoscape from the Windows command prompt and see if there is any output there. 

In addition, there is a log file that is normally located C:\Users\MyName\CytoscapeConfiguration\3 called framework-cytoscape.log. It could contain some additional information, and would be helpful to attach here.

On Friday, October 26, 2018 at 10:15:13 AM UTC-4, Akshaya Biswal wrote: