java.lang.NullPointerException

[trumpets]

Hi guys,

me again

I've been doing a lot of Gephi programming and thinkering and I've encountered a problem. I have a network file, dynamic one, containing ~200 nodes and ~13k edges. When I try to load it in Gephi (0.7beta) I get a popup window with the message "java.lang.NullPointerException". I've tried minimizing the amount of edges and the file loads when the network has ~650 edges... which is really really strange, cause I've seen people on this forum loading ~100k edges!!!

I would really be glad if you could help

Attached you will find the network gexf file!

Thanks!!!

[elijah]

What's your memory set at? I find the more gigabytes I feed my Gephi, the better its attitude.

However, I've received the same error from corrupted .gephi files, so it could be a problem with a particular data point. Have you checked to make sure everything is formatted right and tried to load different pieces of the graph?

[eduramiba]

Hi trumpets,
This exception is being thrown because in your file some edges have an empty target (target="")

The importer could check this and display a more useful message, but it is difficult to have every case in mind

[trumpets]

Thanks eduramiba!! I was suspecting that something was wrong with the file format,and not the amount of nodes/edges

Anyhow, thanks a LOT !
btw, is there a tool or a schema that can validate a gexf file?

[admin]

Yes schemas are available here: http://gexf.net/format/schema.html

[cspenn]

I get this when I try to load a brand new GEXF file.

Gephi 0.8, Mac

Attached is the very simple GEXF file I have, created from Gawk and an Excel Spreadsheet.

Can anyone shed some light on this? All I get once I hit open is the java.lang.NullPointerException dialog box and then nothing at all.

[mbastian]

It seems that some of your edges has no source

Code: Select all

<edge source="" target="cspenn" start="0" end="3600" weight="0">

I just reported a bug to better deal with this case and display proper message.

[gephboardman]

I get this error, too, and none of my edges have target NULL. EDIT, oops sorry, source null.

[Econstudent87]

Hey there,

I have also this error message and when I open Gephi, I can't access the Data laboratory and load any excel spread sheets or anything. I really need help on this since I need to work on a project where I need to conduct a network analysis for a presentation. I run Mac OS X 10.10.1 (14B25), it was working fine until a day ago and I tried to fix it by updating to Java 8, then I thought it might be conflicting with this, so I removed Java 8 and reinstalled Java 7 Update 71.

I am able to load a .gephi file that I already created and I can look at the "Overview" of the network but when selecting "Data Laboratory", nothing shows up at all. I actually need to import network files in .csv to create another network and since I can't access it, I obviously can't do it. Any help is dearly appreciated.

I get this following error code message:

java.lang.NullPointerException
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings.getSuperIdentity(AutoupdateSettings.java:435)
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings.generateIdentity(AutoupdateSettings.java:136)
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateCheckScheduler.signOn(AutoupdateCheckScheduler.java:110)
at org.netbeans.modules.autoupdate.ui.actions.Installer.restored(Installer.java:63)
at org.netbeans.core.startup.NbInstaller.loadCode(NbInstaller.java:469)
[catch] at org.netbeans.core.startup.NbInstaller.loadImpl(NbInstaller.java:392)
at org.netbeans.core.startup.NbInstaller.access$000(NbInstaller.java:103)
at org.netbeans.core.startup.NbInstaller$1.run(NbInstaller.java:344)
at org.openide.filesystems.FileUtil$2.run(FileUtil.java:619)
at org.openide.filesystems.EventControl.runAtomicAction(EventControl.java:127)
at org.openide.filesystems.FileSystem.runAtomicAction(FileSystem.java:607)
at org.openide.filesystems.FileUtil.runAtomicAction(FileUtil.java:603)
at org.openide.filesystems.FileUtil.runAtomicAction(FileUtil.java:623)
at org.netbeans.core.startup.NbInstaller.load(NbInstaller.java:341)
at org.netbeans.ModuleManager.enable(ModuleManager.java:1179)
at org.netbeans.ModuleManager.enable(ModuleManager.java:1002)
at org.netbeans.core.startup.ModuleList.installNew(ModuleList.java:340)
at org.netbeans.core.startup.ModuleList.trigger(ModuleList.java:276)
at org.netbeans.core.startup.ModuleSystem.restore(ModuleSystem.java:296)
at org.netbeans.core.startup.Main.getModuleSystem(Main.java:169)
at org.netbeans.core.startup.Main.start(Main.java:305)
at org.netbeans.core.startup.TopThreadGroup.run(TopThreadGroup.java:123)
at java.lang.Thread.run(Thread.java:695)

Any help how to resolve this and make Gephi work again would be much appreciated.

[giamellaro]

I am having the same problem, same error message. Gephi gets frozen while opening before I can even get to the data lab or any other options- just a grey screen. Interestingly, this only happens when I install gephi into applications. When I open it from within the DMG folder it works fine. This is a good band-aid but I would be interested if figuring out a real solution. I have a feeling it has more to do with java than with Gephi itself.
Thanks