Cytoscape 3.1.1 constant crashing

[Jeff Kiefer]

I am having serious issues trying to run cytoscape 3.1.1. There is really no pattern but it continually gets hung and I need to force quit. I have included a handful of crash reports from my Console. I am running Mac OSX 10.9.3 and Java version 7 (build 1.7.0_60-b19). I have uninstalled cytoscape and apps but that doesn't seem to do much of anything. If anyone out there has an idea it would be greatly appreciated.

Jeff

[Tim Hull]

One thing you could try to see if it resolves the problem would be to delete the CytoscapeConfiguration directory (located in your home directory). This will clear Cytoscape's cache as well as any settings, which may help in the case one of these became corrupted. It will delete any apps you have installed, though.

If that doesn't help, I wonder if it could be a Java issue. Are you running Cytoscape from the terminal (using cytoscape.sh) or the icon? If you are running from the icon, note that Apple Java 6 will always be used regardless of whether Java 7 is installed on your system. 

In either case, I'm curious what version(s) of Java you have installed - certain buggy versions of Java have been known to cause Cytoscape to crash in the past. Could you run the following commands and share the output?

/usr/libexec/java_home -V

echo $JAVA_HOME

Let me know if you get this resolved. If not, having the information about your Java installation would be helpful to troubleshoot this...

Tim

On Mon, Jun 16, 2014 at 2:46 PM, Jeff Kiefer <jeff...@gmail.com> wrote:

I am having serious issues trying to run cytoscape 3.1.1. There is really no pattern but it continually gets hung and I need to force quit. I have included a handful of crash reports from my Console. I am running Mac OSX 10.9.3 and Java version 7 (build 1.7.0_60-b19). I have uninstalled cytoscape and apps but that doesn't seem to do much of anything. If anyone out there has an idea it would be greatly appreciated.

Jeff

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[Jeff Kiefer]

Thanks for replying. The command you had me issue resulted in this:

Matching Java Virtual Machines (2):

    1.6.0_65-b14-462, x86_64: "Java SE 6" /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home

    1.6.0_65-b14-462, i386: "Java SE 6" /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home

I did try to run the .sh file as you suggested. I launched that file using terminal and it fired up cytoscape. Not sure if that was the way or if there is a specific command line instruction to launch. After doing that and working with cytoscape it still got hung up. There must still be something with the Java version. The java version from systems preferences says version 7 but when I check at command line with 'java -version' I get this:

Java(TM) SE Runtime Environment (build 1.6.0_65-b14-462-11M4609)

Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-462, mixed mode)

Something screwy there.

Thanks,

Jeff

On Monday, June 16, 2014 3:40:05 PM UTC-7, Tim Hull wrote:

One thing you could try to see if it resolves the problem would be to delete the CytoscapeConfiguration directory (located in your home directory). This will clear Cytoscape's cache as well as any settings, which may help in the case one of these became corrupted. It will delete any apps you have installed, though.

If that doesn't help, I wonder if it could be a Java issue. Are you running Cytoscape from the terminal (using cytoscape.sh) or the icon? If you are running from the icon, note that Apple Java 6 will always be used regardless of whether Java 7 is installed on your system. 

In either case, I'm curious what version(s) of Java you have installed - certain buggy versions of Java have been known to cause Cytoscape to crash in the past. Could you run the following commands and share the output?

/usr/libexec/java_home -V

echo $JAVA_HOME

Let me know if you get this resolved. If not, having the information about your Java installation would be helpful to troubleshoot this...

Tim

On Mon, Jun 16, 2014 at 2:46 PM, Jeff Kiefer <jeff...@gmail.com> wrote:

I am having serious issues trying to run cytoscape 3.1.1. There is really no pattern but it continually gets hung and I need to force quit. I have included a handful of crash reports from my Console. I am running Mac OSX 10.9.3 and Java version 7 (build 1.7.0_60-b19). I have uninstalled cytoscape and apps but that doesn't seem to do much of anything. If anyone out there has an idea it would be greatly appreciated.

Jeff

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[Tim Hull]

Did you try clearing CytoscapeConfiguration? I'm wondering if the issue couple be related to a corrupt cache/settings - if that was the case, even uninstalling and reinstalling wouldn't fix the issue...

If that doesn't work, could you try downloading the latest Java 7 JDK from Oracle and the latest Java Update from Apple and retrying?  These can be found at the following URLs:

http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html

http://support.apple.com/kb/dl1572

Tim

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[Jeff Kiefer]

I removed the cytoscape config folder when I removed the cytoscape 3.1.1 installation. I also made sure to download the Java 7 JDK and not just JRE. I already had java 6 loaded. I did reload that on to before the java 7. There seems to be some discrepancies in where 6 is stored compared to 7. 6 is in the system/library/java while 7 is in user/library/java. I searched around to see if this might be causing problem in that I might be pointing to 6 and not 7 when launching. I couldn't figure out a fix or if that was causing issues. Anyway, I reinstalled everything and started working. Mainly using BINGO and not having a problem. ClueGO through a out of memory error and that froze my session. I did do some looking in cytoscape associated files and found the i4jlauncher file (attached) that seemed to record some records regarding some Java issues. Not sure if this is informative.

Thanks,

Jeff

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[Tim Hull]

That file looks like a generic string file used internally by Install4J - it doesn't seem to refer to your specific problem.

As for the ClueGO crash, is it something you can reproduce? If so, what do you have to do to make it happen, and what is the full error message that you see? 

Tim

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[Jeff Kiefer]

The ClueGO crash happens right after the results of selected analysis is written to results panel. The ClueGO job bars go to about 88% after writing to results panel and then freezes. I have increased memory in my 
Cytoscape.vmoptions file to -Xmx5G, so I wouldn't think that would be a problem. I do not see any error message. Is that written to a file somewhere? I do not see it in console but might not be looking in the right place.

Thanks,

Jeff

[Tim Hull]

Since you're on a Mac, running Cytoscape from the icon won't use the memory value in Cytoscape.vmoptions - instead, you will have to edit the .Contents/Info.plist file (inside the Cytoscape app bundle - right-click on it and choose Show Package Contents.

If that doesn't help, I'd try contacting the ClueGO team to see if they can help, as this seems like it may be a ClueGO-specific issue. The contact listed on the App Store is gabriel...@crc.jussieu.fr

Hope this helps...

Tim

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[Jeff Kiefer]

Thanks for the heads up with the contact list person. I did have the memory changed also in plist file. There are just some funky things going on still. I have issues with cytoscape 2.8.3, such as freezing when trying to open .xgmml files. I also have issues if I launch cityscape (2.8.3 or 3.1.1) by opening cytoscape.sh with terminal. You had mentioned that it should launch with java 7 but after terminal launch and 'info' command it is listing java 1.6.0_65 even though java JDK 7 is installed. Do you think there are issues around that.

thanks,

JK

[Tim Hull]

This is a known issue - on Mac, Java 6 is used by Cytoscape even if Java 7 is available unless the JAVA_HOME environment variable is set to point to Java 7. The issue (including a workaround) is discussed further in the Release Notes for Cytoscape 3.1.1:

http://www.cytoscape.org/release_notes_3_1_1.html

Note that even after setting the JAVA_HOME variable, running Cytoscape using the icon will still use Java 6. You will have to run from cytoscape.sh to use Java 7.

Tim

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[Jeff Kiefer]

Hi Tim,

So, I edited the .bashrc and .profile files with required text and opened cytoscape from command line. Running info command still lists Java 6 as my version. Running the ' /usr/libexec/java_home -V echo $JAVA_HOME ' returns:

Matching Java Virtual Machines (3):

    1.7.0_60, x86_64: "Java SE 7" /Library/Java/JavaVirtualMachines/jdk1.7.0_60.jdk/Contents/Home

    1.6.0_65-b14-466.1, x86_64: "Java SE 6" /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home

    1.6.0_65-b14-466.1, i386: "Java SE 6" /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home

I don't see why it still is running through Java 6.

I also checked and the bashrc and profile files do not have any other text, except for what I put in them. Also, went through reboot on whole system.

JK

[Tim Hull]

Hi,

"/usr/libexec/java_home -V" and "echo $JAVA_HOME" are two separate commands. Could you try closing/restarting all Terminal windows and the system again and then run "echo $JAVA_HOME" in the Terminal to see what it shows? It should show the path to Java 7 (same as in the output you pasted above).

If at that point it shows a Java 6 path - or no path at all - something is wrong with your .bashrc/.profile files. I would check to make sure they are properly named (note that the dot before bashrc/profile is essential), and located in the root of your home directory. If you used TextEdit to create them, it may have added an extension and/or saved in RTF format - I would use a command line text editor (nano/vi/emacs or the like) to make sure they're plain text and have no added extension. 

If at that point everything looks fine and it still doesn't work, I'd check to make sure the content is right. I've attached example files for both .bashrc and .profile - not that I had to remove the dot from the file name to easily attach to the e-mail...

Hope this helps...

Tim

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[Jeff Kiefer]

I went nuclear and wiped me computer and reinstalled a clean OSX. I had the correct files in the root with no extensions and made with nano. Anyway, let's hope this works. For Java would you advise to install Java 7 or go with default 6 (I believe 6 is installed by default but could be wrong)?

JK

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<bashrc>

<profile>

[Tim Hull]

Did you put the files in the root of the user home directory (i.e. /Users/Yourname/, or ~ for short) or the main root ( just / )? It needs to be in the user home directory...

In any case, I doubt reinstalling is going to make a difference unless there is something seriously wrong with your system - which I don't think is the case based on what you have described. As for Java 6 vs 7, it doesn't make a big difference unless you want to develop/run apps requiring Java 7. Also, even after reinstalling, you're going to have to set up the JAVA_HOME in the same way.

Tim

[Jeff Kiefer]

Okay. Finished everything up. I did put the two files in the right directory using Nano editor previously. After system redo, I put them back in. Before that I installed java 7 jdk. Downloaded latest version of cityscape 3.1.1 and began install. It asked for apple java 6. Installed that. Then made the two files .bashrc and .profile. Launched cityscape from command line, issued info command and success it is listing java 1.7. I am now going to move forward and start seeing if any of the crashes still happen.

Will keep you posted.

thanks,

Jeff

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<bashrc>

<profile>

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