Launch error in Ubuntu 10.04 LTS

Hi,

Could you please look if you have a message log file in your user directory ? Thanks.

/home/username/.gephidesktop/var/log

Hi Mathieu,

Thanks for your kind follow up.

Please observe below the message logged:

-------------------------------------------------------------------------------
>Log Session: Friday, June 4, 2010 2:48:09 PM CEST
>System Info:
  Product Version = Gephi 0.7 alpha4 200912041610
  Operating System = Linux version 2.6.32-22-generic running on i386
  Java; VM; Vendor = 1.6.0_20; Java HotSpot(TM) Server VM 16.3-b01; Sun Microsystems Inc.
  Runtime = Java(TM) SE Runtime Environment 1.6.0_20-b02
  Java Home = /usr/lib/jvm/java-6-sun-1.6.0.20/jre
  System Locale; Encoding = en_US (gephidesktop); UTF-8
  Home Directory = /root
  Current Directory = /media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/bin
  User Directory = /home/nima/.gephidesktop/dev
  Installation = /media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/gephidesktop
                            /media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/platform11
  Boot & Ext. Classpath = /usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/resources.jar:/usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/rt.jar:/usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/sunrsasign.jar:/usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/jsse.jar:/usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/jce.jar:/usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/charsets.jar:/usr/lib/jvm/java-6-sun-1.6.0.20/jre/classes:/usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/ext/dnsns.jar:/usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/ext/sunpkcs11.jar:/usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/ext/localedata.jar:/usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/ext/sunjce_provider.jar
  Application Classpath = /media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/platform11/lib/boot.jar:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/platform11/lib/org-openide-modules.jar:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/platform11/lib/org-openide-util.jar:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/platform11/lib/locale/org-openide-util_ja.jar:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/platform11/lib/locale/org-openide-util_pt_BR.jar:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/platform11/lib/locale/org-openide-util_zh_CN.jar:/usr/lib/jvm/java-6-sun/lib/dt.jar:/usr/lib/jvm/java-6-sun/lib/tools.jar
  Startup Classpath = /media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/platform11/core/core.jar:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/platform11/core/org-openide-filesystems.jar:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/bin/./../gephidesktop/core/locale/core_gephidesktop.jar
-------------------------------------------------------------------------------
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/gephidesktop/modules/org-gephi-graph-api.jar!/org/gephi/graph/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/gephidesktop/modules/org-gephi-data-attributes-api.jar!/org/gephi/data/attributes/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/gephidesktop/modules/org-gephi-layout-api.jar!/org/gephi/layout/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/gephidesktop/modules/org-gephi-layout-plugin.jar!/org/gephi/layout/plugin/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/gephidesktop/modules/org-gephi-preview-api.jar!/org/gephi/preview/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/gephidesktop/modules/org-gephi-io-importer-api.jar!/org/gephi/io/importer/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/gephidesktop/modules/org-gephi-ui-components.jar!/org/gephi/ui/components/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/gephidesktop/modules/org-gephi-io-importer-plugin.jar!/org/gephi/io/importer/plugin/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/gephidesktop/modules/org-gephi-tools-api.jar!/org/gephi/tools/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/gephidesktop/modules/org-gephi-filters-api.jar!/org/gephi/filters/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/gephidesktop/modules/org-gephi-statistics-api.jar!/org/gephi/statistics/api/layer.xml
java.lang.ClassFormatError: Unknown constant tag 97 in class file org/openide/loaders/UniFileLoader
 at java.lang.ClassLoader.defineClass1(Native Method)
 at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
 at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
 at org.netbeans.JarClassLoader.doLoadClass(JarClassLoader.java:246)
 at org.netbeans.ProxyClassLoader.selfLoadClass(ProxyClassLoader.java:297)
 at org.netbeans.ProxyClassLoader.loadClass(ProxyClassLoader.java:224)
 at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
 at java.lang.ClassLoader.defineClass1(Native Method)
 at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
 at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
 at org.netbeans.JarClassLoader.doLoadClass(JarClassLoader.java:246)
 at org.netbeans.ProxyClassLoader.selfLoadClass(ProxyClassLoader.java:297)
 at org.netbeans.ProxyClassLoader.loadClass(ProxyClassLoader.java:224)
 at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
 at org.openide.loaders.DataLoaderPool.getSystemLoaders(DataLoaderPool.java:674)
 at org.openide.loaders.DataLoaderPool.computeLoaders(DataLoaderPool.java:281)
 at org.openide.loaders.DataLoaderPool.allLoaders(DataLoaderPool.java:332)
 at org.openide.loaders.DataLoaderPool.findDataObject(DataLoaderPool.java:526)
 at org.openide.loaders.DataLoaderPool.findDataObject(DataLoaderPool.java:489)
 at org.openide.loaders.DataObject.find(DataObject.java:506)
 at org.openide.loaders.DataFolder.findFolder(DataFolder.java:550)
 at org.netbeans.core.CoreBridgeImpl.lookupCacheLoad(CoreBridgeImpl.java:129)
 at org.netbeans.core.startup.MainLookup.doInitializeLookup(MainLookup.java:185)
 at org.netbeans.core.startup.MainLookup.modulesClassPathInitialized(MainLookup.java:145)
 at org.netbeans.core.startup.NbInstaller.load(NbInstaller.java:351)
 at org.netbeans.ModuleManager.enable(ModuleManager.java:928)
 at org.netbeans.core.startup.ModuleList.installNew(ModuleList.java:289)
 at org.netbeans.core.startup.ModuleList.trigger(ModuleList.java:225)
 at org.netbeans.core.startup.ModuleSystem.restore(ModuleSystem.java:276)
 at org.netbeans.core.startup.Main.getModuleSystem(Main.java:168)
 at org.netbeans.core.startup.Main.start(Main.java:309)
 at org.netbeans.core.startup.TopThreadGroup.run(TopThreadGroup.java:111)
 at java.lang.Thread.run(Thread.java:619)

guys any progress W R T my problem ? is this a bug ?

This is weird, it's like the system still have input pointers to OpenJDK. Perhaps you could try to remove all java install, clean the remaining repositories (could be dangerous), and install Java again.

I'm sorry but I don't have a better idea.

If it could be of help, I saw a similar problem (ClassFormatError: Unknown constant tag) with corrupted class files a long time ago. Maybe we could try to verify the integrity of the platform jars. For this, you could run the following command:
md5sum /media/officebuntu2/visualization/gephi/gephi-0.7-alpha4/platform11/modules/*
and we could try to compare the checksums with the original ones.
Or you could try to download Gephi and install all over again...
By the way, I'm using Ubuntu 10.04 LTS with java-6-sun-1.6.0.20 with no problems.

Hi all,

I was having the exact same problem (run Ubuntu 10.04 with same java version) when launching Gephi. On the other side I also had issues with gzip, which turned to be related to the issue I had with Gephi. Indeed, when looking at the error messages thrown in the terminal I saw some problems with reading the jar archives.
 So I went on trying to solve the gzip issue (It was sending me errors when unarchiving ... the gephi archive by the way) which I did by installing gzip 1.4 from source, following indications from : https://bugs.launchpad.net/ubuntu/+source/gzip/+bug/524366.

And now both unarchiving and running Gephi work :)

Hi people, thanks for your attention.

now something new happened!
I downloaded the tar.gz file of 7 alpha 4 (recent version) and when I try to gunzip it I get this:
....
gephi-0.7-alpha4/platform11/update_tracking/org-openide-modules.xml
gephi-0.7-alpha4/platform11/update_tracking/org-openide-nodes.xml
gephi-0.7-alpha4/platform11/update_tracking/org-openide-text.xml
gephi-0.7-alpha4/platform11/update_tracking/org-openide-util.xml
gephi-0.7-alpha4/platform11/update_tracking/org-openide-windows.xml
tar: Child returned status 1
tar: Exiting with failure status due to previous errors

I tried downloading 7 alpha 3 and I get the same error.

Although I got the linux version of 0.6beta3 release and gephi comes up pretty easily.
Downside is lots of things have changed since this version !

Yes, that's what I was running into as well.

I think your issue has to do with a bug in the gzip package (or gunzip, 'don't remember). So try fixing the gzip issue (see my previous post) and hopefully you'll then be able to run gephi.

I can confirm that your most recent problem (trying to install gephi-0.7-alpha4.tar.gz) is caused by the current version of gzip in Ubuntu 10.4 Lucid, and NOT by Gephi.
(For details pls see: https://bugs.launchpad.net/ubuntu/+source/gzip/+bug/524366 )

A solution is to unpack the tar.gz on another system (that doesn't use Ubuntu 10.4) and then copy the directory back to your home Ubuntu 10.4 machine. (note: you can also do this over ssh on your university server and copy the result back) It worked for me!

Wouldn't it be possible to provide a ZIP file? Many people are using Ubuntu 10.04 nowadays...

@ Philip: although what you suggest would solve the problem for ubuntu 10.4 users at the moment, the real problem is the before-mentioned bug in gzip. As such, as a fellow Ubuntu user I would like to ask you and other users to go to the launchpad page and click on "this bug effects me" etc. so the developers of gzip know that there is a higher urgency to fix the problem (and have the fix available in the Update Manager). Tnx! ;-)

Thanks, I have followed your instructions.

By the way, in the meantime I have extracted the archive with 7zip:

sudo apt-get install p7zip-full

7z x gephi-0.7-alpha4.tar.gz

I also confirm that the error is caused by the current version of gzip and can be solved installing the proposed package as described here: https://bugs.launchpad.net/ubuntu/+source/gzip/+bug/524366 Should be available soon as regular update. Thanks for your hints!