could not finish layout

[Maria Carolina Medina]

Dear all I was using cytoscape 3.3 few weeks ago and it was working fine... now everytime I try to upload a table I receive the error message "Could not finish layout"... I can still open my saved sessions and they look fine, but everythime I try to load a new table I cannot due to the error message.

My java is 1.8.0_77...

Best regards, Carolina 

[Barry Demchak]

Thanks, Carolina …

 

Any chance you could send us the file and a list of the steps you used?

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[Maria Carolina Medina]

Sure... I am using DEPICT to produce the gene network by DEPICT software I obtain four files. A network file, a node attributes file, a cluster results and a cytoscape script.

I could never make the script run... It always produced the same error ( ,eval.1:8 ).. but I managed in any case to create the style and make manually the import of the tables. I saved the session (attached).

The issue is now when I try to read the same network table as I did in that session I get the error I mentioned (actually I want to depict other network but as that one was functioning tried with that one as well). So I go to cytoscape 3.3. or 3.4 in windows opened and in the first dialogue "I select start new session from network file " and upload my file but inmediately the 

Please find attached all my files, thanks a lot. Carolina 

On Tuesday, August 16, 2016 at 4:10:58 PM UTC+2, Barry Demchak wrote:

Thanks, Carolina …

 

Any chance you could send us the file and a list of the steps you used?

 

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Maria Carolina Medina
Sent: Tuesday, August 16, 2016 5:48 AM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] could not finish layout

 

Dear all I was using cytoscape 3.3 few weeks ago and it was working fine... now everytime I try to upload a table I receive the error message "Could not finish layout"... I can still open my saved sessions and they look fine, but everythime I try to load a new table I cannot due to the error message.

 

My java is 1.8.0_77...

 

Best regards, Carolina 

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[Tim Hull]

I tried importing the network table file into a new session and never saw the error message, and was also able to import the node attributes without any problem. When are you seeing this error? Is it when you import the network, or later? 

Tim

On Tue, Aug 16, 2016 at 8:52 AM, Maria Carolina Medina <medina.mar...@gmail.com> wrote:

Sure... I am using DEPICT to produce the gene network buy DEPICT I obtain four files. A network file, a node attributes file, a cluster results and a cytoscape script.

I could never make the script run... It alwys produced the same error ( ,eval.1:8 ).. but I managed in any case to create the style and make manually the import of the tables. I saved the session (attached).

The issue is now when I try to read the same network table as I did in that session I get the error I mentioned (actually I want to depict other network but as that one was functioning tried with that one as well). So I go to cytoscape 3.3. or 3.4 in windows opened and in the first dialogue "I select start new session from network file " and upload my file but inmediately the 

Please find attached all my files, thanks a lot. Carolina 

On Tuesday, August 16, 2016 at 4:10:58 PM UTC+2, Barry Demchak wrote:

Thanks, Carolina …

 

Any chance you could send us the file and a list of the steps you used?

 

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Maria Carolina Medina
Sent: Tuesday, August 16, 2016 5:48 AM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] could not finish layout

 

Dear all I was using cytoscape 3.3 few weeks ago and it was working fine... now everytime I try to upload a table I receive the error message "Could not finish layout"... I can still open my saved sessions and they look fine, but everythime I try to load a new table I cannot due to the error message.

 

My java is 1.8.0_77...

 

Best regards, Carolina 

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[Maria Carolina Medina]

Dear Tim as soon as I try to import please find an screenshot... no idea what could be going wrong

On Tuesday, August 16, 2016 at 7:23:35 PM UTC+2, Tim Hull wrote:

I tried importing the network table file into a new session and never saw the error message, and was also able to import the node attributes without any problem. When are you seeing this error? Is it when you import the network, or later? 

Tim

On Tue, Aug 16, 2016 at 8:52 AM, Maria Carolina Medina <medina.mar...@gmail.com> wrote:

Sure... I am using DEPICT to produce the gene network buy DEPICT I obtain four files. A network file, a node attributes file, a cluster results and a cytoscape script.

I could never make the script run... It alwys produced the same error ( ,eval.1:8 ).. but I managed in any case to create the style and make manually the import of the tables. I saved the session (attached).

The issue is now when I try to read the same network table as I did in that session I get the error I mentioned (actually I want to depict other network but as that one was functioning tried with that one as well). So I go to cytoscape 3.3. or 3.4 in windows opened and in the first dialogue "I select start new session from network file " and upload my file but inmediately the 

Please find attached all my files, thanks a lot. Carolina 

On Tuesday, August 16, 2016 at 4:10:58 PM UTC+2, Barry Demchak wrote:

Thanks, Carolina …

 

Any chance you could send us the file and a list of the steps you used?

 

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Maria Carolina Medina
Sent: Tuesday, August 16, 2016 5:48 AM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] could not finish layout

 

Dear all I was using cytoscape 3.3 few weeks ago and it was working fine... now everytime I try to upload a table I receive the error message "Could not finish layout"... I can still open my saved sessions and they look fine, but everythime I try to load a new table I cannot due to the error message.

 

My java is 1.8.0_77...

 

Best regards, Carolina 

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[Tim Hull]

This happens when you import right after starting/restarting Cytoscape, correct? Are you importing from tophitsnonstrict194_tissueenrichment_network_table.txt? 

If that is indeed the case, I had one thought - did you ever change the default layout of Cytoscape? If so, there may be an issue with that layout that prevents it from finishing. Importing this file works OK here with the normal default layout, so I'm a bit perplexed - particularly since it isn't a complex network. Does this problem happen when you import one of the sample networks in the sampleData directory of the Cytoscape installation (like galFiltered.sif)?

If it's not the layout, can you run Cytoscape from the command line (cytoscape.bat) and copy/paste any error messages you get on the console?

Hope this helps...

Tim

On Tue, Aug 16, 2016 at 10:34 AM, Maria Carolina Medina <medina.mar...@gmail.com> wrote:

Dear Tim as soon as I try to import please find an screenshot... no idea what could be going wrong

On Tuesday, August 16, 2016 at 7:23:35 PM UTC+2, Tim Hull wrote:

I tried importing the network table file into a new session and never saw the error message, and was also able to import the node attributes without any problem. When are you seeing this error? Is it when you import the network, or later? 

Tim

On Tue, Aug 16, 2016 at 8:52 AM, Maria Carolina Medina <medina.mar...@gmail.com> wrote:

Sure... I am using DEPICT to produce the gene network buy DEPICT I obtain four files. A network file, a node attributes file, a cluster results and a cytoscape script.

I could never make the script run... It alwys produced the same error ( ,eval.1:8 ).. but I managed in any case to create the style and make manually the import of the tables. I saved the session (attached).

The issue is now when I try to read the same network table as I did in that session I get the error I mentioned (actually I want to depict other network but as that one was functioning tried with that one as well). So I go to cytoscape 3.3. or 3.4 in windows opened and in the first dialogue "I select start new session from network file " and upload my file but inmediately the 

Please find attached all my files, thanks a lot. Carolina 

On Tuesday, August 16, 2016 at 4:10:58 PM UTC+2, Barry Demchak wrote:

Thanks, Carolina …

 

Any chance you could send us the file and a list of the steps you used?

 

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Maria Carolina Medina
Sent: Tuesday, August 16, 2016 5:48 AM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] could not finish layout

 

Dear all I was using cytoscape 3.3 few weeks ago and it was working fine... now everytime I try to upload a table I receive the error message "Could not finish layout"... I can still open my saved sessions and they look fine, but everythime I try to load a new table I cannot due to the error message.

 

My java is 1.8.0_77...

 

Best regards, Carolina 

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[Maria Carolina Medina]

Yes same error message when trying with galFiltered.sif, actually I thought I messed up things... reason why I today downloaded Cytoscape 3.4 (without uninstalling Cytoscape 3.3)... so then as it is newly downloaded I had not even run an analysis there (no probability I change anything I guess).

I also tried runing the .bat file as you suggested here the error message:

Cytoscape 3.4.0

Hit '<tab>' for a list of available commands

   and '[cmd] --help' for help on a specific command.

Hit '<ctrl-d>' or 'osgi:shutdown' to shutdown Cytoscape.

Cytoscape 3.4.0> ======= cyREST Initialization start ======

Retry: 0

java.lang.RuntimeException: Could not finish layout

        at org.cytoscape.io.internal.read.sif.SIFNetworkReader.buildCyNetworkVie

w(SIFNetworkReader.java:205)

        at org.cytoscape.task.internal.loadnetwork.GenerateNetworkViewsTask.crea

teNetworkView(GenerateNetworkViewsTask.java:182)

        at org.cytoscape.task.internal.loadnetwork.GenerateNetworkViewsTask.run(

GenerateNetworkViewsTask.java:114)

        at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.inne

rRun(JDialogTaskManager.java:342)

        at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(

JDialogTaskManager.java:355)

        at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)

        at java.util.concurrent.FutureTask.run(Unknown Source)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)

        at java.lang.Thread.run(Unknown Source)

Caused by: java.lang.NullPointerException

        at csapps.layout.algorithms.GroupAttributesLayoutTask.construct(GroupAtt

ributesLayoutTask.java:107)

        at csapps.layout.algorithms.GroupAttributesLayoutTask.doLayout(GroupAttr

ibutesLayoutTask.java:73)

        at org.cytoscape.view.layout.AbstractLayoutTask.run(AbstractLayoutTask.j

ava:156)

        at org.cytoscape.io.internal.read.sif.SIFNetworkReader.buildCyNetworkVie

w(SIFNetworkReader.java:203)

        ... 9 more

Thanks a lot. 

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[Tim Hull]

It looks like your default layout somehow got changed to "Group Attributes Layout", which requires an attribute selection and as such produces the error you described when using it as a default layout. To resolve this, change the default layout - either to "Prefuse Force Directed" (the default) or another layout that does not require a parameter. You can do that in the "Preferred Layout" tab on the Layout-Settings... dialog.

Let me know if this resolves the issue...

Tim

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[Maria Carolina Medina]

you are great thanks... no idea how I managed to do that!

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[Mike Kucera]

Similar to bug #3230

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