Gephi forums

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!!!

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?

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

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?

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

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.

It seems that some of your edges has no source
I just reported a bug to better deal with this case and display proper message.

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

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.

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