Gephi

Cannot get gephi to load on MacBook

Asked by Stefani Crabtree

Hello,
I installed gephi according to the instructions on line. I have java 6 and have followed all of your FAQ's, but I still cannot get it to work. One other person in my lab has the same problem. Gephi installs fine, and I load one of the sample files. When the file loads on the upper right hand screen I can see the number of nodes and edges. However, on the screen there is no display, I cannot alternate among overview, data laboratory and preview and I have a spinning blue ball. I have a MacBook Pro, one year old. Please let me know what to do.

Thanks for all of your help,

Stefani

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Sébastien Heymann (sebastien.heymann) said : 		#1

Hi,

Can you post the log file?

You'll find it on /username/Library/Application support/gephi/dev/var/log/messages.log

Thanks

Revision history for this message
Stefani Crabtree (stefanicrabtree) said : 		#2

Here is the log file:
-------------------------------------------------------------------------------
>Log Session: Wednesday, June 15, 2011 8:10:40 AM PDT
>System Info:
   Product Version = Gephi 0.8 alpha
  Operating System = Mac OS X version 10.6.7 running on x86_64
  Java; VM; Vendor = 1.6.0_24; Java HotSpot(TM) 64-Bit Server VM 19.1-b02-334; Apple Inc.
  Runtime = Java(TM) SE Runtime Environment 1.6.0_24-b07-334-10M3326
  Java Home = /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
  System Locale; Encoding = en_US (gephi); MacRoman
  Home Directory = /Users/stefanicrabtree
  Current Directory = /
  User Directory = /Users/stefanicrabtree/Library/Application Support/gephi/dev
  Installation = /Applications/gephi.app/Contents/Resources/gephi/gephi
                            /Applications/gephi.app/Contents/Resources/gephi/platform
  Boot & Ext. Classpath = /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jsfd.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/classes.jar:/System/Library/Frameworks/JavaVM.framework/Frameworks/JavaRuntimeSupport.framework/Resources/Java/JavaRuntimeSupport.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/ui.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/laf.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/sunrsasign.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jsse.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jce.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/charsets.jar:/Library/Java/Extensions/gluegen-rt.jar:/Library/Java/Extensions/j3dcore.jar:/Library/Java/Extensions/j3dutils.jar:/Library/Java/Extensions/jogl.jar:/Library/Java/Extensions/vecmath.jar:/System/Library/Java/Extensions/AppleScriptEngine.jar:/System/Library/Java/Extensions/dns_sd.jar:/System/Library/Java/Extensions/j3daudio.jar:/System/Library/Java/Extensions/j3dcore.jar:/System/Library/Java/Extensions/j3dutils.jar:/System/Library/Java/Extensions/jai_codec.jar:/System/Library/Java/Extensions/jai_core.jar:/System/Library/Java/Extensions/mlibwrapper_jai.jar:/System/Library/Java/Extensions/MRJToolkit.jar:/System/Library/Java/Extensions/QTJava.zip:/System/Library/Java/Extensions/vecmath.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/ext/apple_provider.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/ext/dnsns.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/ext/localedata.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/ext/sunjce_provider.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/ext/sunpkcs11.jar
  Application Classpath = /Applications/gephi.app/Contents/Resources/gephi/platform/lib/boot.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/org-openide-modules.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/org-openide-util-lookup.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/org-openide-util.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ar_SA.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_pt_PT.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_sq.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_zh_TW.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ar_SA.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_pt_PT.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_sq.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_zh_TW.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ar_SA.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_pt_PT.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_sq.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_zh_TW.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/dt.jar
  Startup Classpath = /Applications/gephi.app/Contents/Resources/gephi/platform/core/core.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/org-openide-filesystems.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ar_SA.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_pt_PT.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_sq.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_zh_TW.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ar_SA.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_pt_PT.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_sq.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_zh_TW.jar:/Applications/gephi.app/Contents/MacOS/../Resources/gephi/bin/../gephi/core/locale/core_gephi.jar
-------------------------------------------------------------------------------
INFO [org.netbeans.core.startup.NbEvents]: Turning on modules:
 org.openide.util.lookup [8.6.1 201103280000]
 org.openide.util [8.14.1 201103280000]
 org.openide.modules [7.22.1 201103280000]
 org.openide.filesystems [7.46.1 201103280000]
 org.openide.awt [7.30.1 201103280000]
 org.netbeans.api.progress/1 [1.23.1 201103280000]
 org.openide.dialogs [7.18.1 201103280000]
 org.openide.nodes [7.20.1 201103280000]
 org.openide.windows [6.39.1 201103280000]
 org.netbeans.modules.editor.mimelookup/1 [1.21.1 201103280000]
 org.openide.text [6.36.1 201103280000]
 org.netbeans.swing.tabcontrol [1.24.1 201103280000]
 org.netbeans.swing.outline [1.13.1 201103280000]
 org.openide.explorer [6.34.1 201103280000]
 org.openide.actions [6.21.1 201103280000]
 org.netbeans.modules.queries/1 [1.22.1 201103280000]
 org.openide.loaders [7.20.1 201103280000]
 org.openide.io [1.26.1 201103280000]
 org.netbeans.swing.plaf [1.19.1 201103280000]
 org.netbeans.swing.dirchooser [1.1 110412]
 org.netbeans.api.annotations.common/1 [1.8.1 201103280000]
 org.netbeans.spi.quicksearch [1.9.1 201103280000]
 org.netbeans.bootstrap/1 [2.39.1 201103280000]
 org.netbeans.core.startup/1 [1.29.1 201103280000]
 org.netbeans.modules.settings/1 [1.30.1 201103280000]
 org.netbeans.modules.sendopts/2 [2.12.1 201103280000]
 org.netbeans.modules.progress.ui [1.15.1 201103280000]
 org.netbeans.modules.print [7.8.1 201103280000]
 org.netbeans.modules.keyring [1.5.1 201103280000]
 org.netbeans.core/2 [3.24.1 201103280000]
 org.netbeans.modules.options.api/1 [1.21.1 201103280000]
 org.netbeans.modules.options.keymap [1.13.1 201103280000]
 org.netbeans.libs.jna/1 [1.13.1 201103280000]
 org.netbeans.modules.masterfs/2 [2.31.1 201103280000]
 org.netbeans.modules.keyring.impl [1.2.1 201103280000]
 org.netbeans.modules.favorites/1 [1.24.1 201103280000]
 org.netbeans.modules.editor.mimelookup.impl/1 [1.13.1 201103280000]
 org.netbeans.modules.autoupdate.services [1.25.1 201103280000]
 org.netbeans.modules.autoupdate.ui [1.22.1 201103280000]
 org.netbeans.core.windows/2 [2.27.1 201103280000]
 org.netbeans.modules.applemenu/1 [1.19.1 201103280000]
 org.netbeans.libs.junit4 [1.13 201103280000]
 org.netbeans.core.ui/1 [1.26.1 201103280000]
 org.netbeans.core.nativeaccess/1 [1.11.1 201103280000]
 org.netbeans.core.io.ui/1 [1.11.1 201103280000]
 org.joda.time [1.0 110412]
 org.jfree [1.0 110412]
 org.jdesktop.swingx [1.6.1 110412]
 org.gephi.lib.javacsv [2.0 110412]
 org.gephi.utils.longtask [0.8 110412]
 org.gephi.project.api [0.8 110412]
 org.gephi.graph.api [0.8 110412]
 org.gephi.data.attributes.api [0.8 110412]
 org.gephi.dynamic.api [0.8 110412]
 org.gephi.utils [0.8 110412]
 org.gephi.datalab.api [0.8.0.1 110605]
 org.gephi.visualization.api [0.8 110412]
 org.gephi.tools.api [0.8.0.1 110522]
 org.gephi.lib.validation [0.4 110412]
 org.gephi.ui.utils [0.8 110412]
 org.gephi.lib.gleem [1.0 110412]
 org.gephi.lib.jogl [1.1.0.1 110412]
 org.gephi.utils.collection [0.8.0.1 110507]
 org.gephi.lib.flamingo [5.0.1 110412]
 org.gephi.lib.commons.codec [1.4 110412]
 org.gephi.ui.components [0.8 110412]
 org.gephi.lib.commonscompress [1.1 110412]
 org.gephi.io.database.drivers [0.8 110412]
 org.gephi.io.importer.api [0.8 110412]
 org.gephi.desktop.mrufiles.api [0.8 110412]
 org.gephi.desktop.project [0.8 110412]
 org.gephi.visualization [0.8.0.1 110605]
 org.gephi.ui.workspace [0.8 110412]
 org.gephi.statistics.api [0.8 110412]
 org.gephi.statistics.plugin [0.8.0.2 110605]
 org.gephi.ui.statistics.plugin [0.8.0.2 110605]
 org.gephi.lib.jcalendar [1.0 110412]
 org.gephi.lib.javamail [1.0 110412]
 org.gephi.io.spigot.plugin [0.8 110412]
 org.gephi.ui.spigot.plugin [0.8 110412]
 org.gephi.ranking.api [0.8 110412]
 org.gephi.ui.ranking.plugin [0.8 110412]
 org.gephi.ui.propertyeditor [0.8 110412]
 org.gephi.ui.project [0.8 110412]
 org.gephi.lib.beansbinding [1.2.1 110412]
 org.gephi.io.processor.plugin [0.8 110412]
 org.gephi.ui.processor.plugin [0.8 110412]
 org.gephi.partition.api [0.8 110412]
 org.gephi.partition.plugin [0.8 110412]
 org.gephi.ui.partition.plugin [0.8 110412]
 org.gephi.io.importer.plugin [0.8 110412]
 org.gephi.ui.importer.plugin [0.8 110412]
 org.gephi.io.generator.api [0.8 110412]
 org.gephi.io.generator.plugin [0.8 110412]
 org.gephi.ui.generator.plugin [0.8 110412]
 org.gephi.filters.api [0.8 110412]
 org.gephi.timeline [0.8 110412]
 org.gephi.filters.plugin [0.8.0.1 110605]
 org.gephi.ui.filters.plugin [0.8 110412]
 org.gephi.lib.itext [5.0.1 110412]
 org.gephi.io.exporter.api [0.8 110412]
 org.gephi.lib.batik [1.7 110412]
 org.gephi.preview.api [0.8 110412]
 org.gephi.io.exporter.preview [0.8 110412]
 org.gephi.ui.exporter.preview [0.8 110412]
 org.gephi.lib.staxutils [1.0 110412]
 org.gephi.io.exporter.plugin [0.8 110412]
 org.gephi.ui.exporter.plugin [0.8 110412]
 org.gephi.ui.components.SplineEditor [0.8 110412]
 org.gephi.algorithms [0.8 110412]
 org.gephi.desktop.perspective [0.8 110412]
 org.gephi.tools.plugin [0.8 110412]
 org.gephi.lib.processing [1.0.9 110412]
 org.gephi.preview [0.8.0.2 110605]
 org.gephi.layout.api [0.8.0.1 110522]
 org.gephi.layout.plugin [0.8.0.2 110605]
 org.gephi.graph.dhns [0.8 110412]
 org.gephi.filters [0.8 110412]
 org.gephi.dynamic [0.8 110412]
 org.gephi.desktop.welcome [0.8 110412]
 org.gephi.desktop.tools [0.8.0.1 110605]
 org.gephi.desktop.timeline [0.8 110412]
 org.gephi.desktop.statistics [0.8 110412]
 org.gephi.desktop.spigot [0.8 110412]
 org.gephi.desktop.recentfiles [1.0.1 110412]
 org.gephi.desktop.ranking [0.8 110412]
 org.gephi.desktop.progress [0.8 110412]
 org.gephi.desktop.io.export [0.8 110412]
 org.gephi.desktop.preview [0.8 110412]
 org.gephi.desktop.partition [0.8 110412]
 org.gephi.desktop.layout [0.8.0.1 110522]
 org.gephi.desktop.importer [0.8.0.1 110605]
 org.gephi.desktop.hierarchy [0.8 110412]
 org.gephi.desktop.generate [0.8 110412]
 org.gephi.desktop.filters [0.8 110412]
 org.gephi.desktop.datalab [0.8.0.2 110605]
 org.gephi.desktop.context [0.8 110412]
 org.gephi.clustering.api [0.8 110412]
 org.gephi.desktop.clustering [0.8 110412]
 org.gephi.datalab.plugin [0.8.0.2 110605]
 org.gephi.data.attributes [0.8 110412]
 org.gephi.clustering.plugin [0.8 110412]
 org.gephi.branding.desktop [0.8.0.1 110412]
Loading native libraries
SEVERE [global]
java.lang.UnsatisfiedLinkError: com.sun.opengl.impl.JAWTFactory.JAWT_GetAWT0(Ljava/nio/ByteBuffer;)Z
 at com.sun.opengl.impl.JAWTFactory.JAWT_GetAWT0(Native Method)
 at com.sun.opengl.impl.JAWTFactory.JAWT_GetAWT(JAWTFactory.java:38)
 at com.sun.opengl.impl.JAWT$1.run(JAWT.java:99)
 at java.security.AccessController.doPrivileged(Native Method)
 at com.sun.opengl.impl.JAWT.getJAWT(JAWT.java:95)
 at com.sun.opengl.impl.macosx.MacOSXOnscreenGLDrawable.lockSurface(MacOSXOnscreenGLDrawable.java:144)
 at com.sun.opengl.impl.macosx.MacOSXOnscreenGLContext.makeCurrentImpl(MacOSXOnscreenGLContext.java:57)
 at com.sun.opengl.impl.GLContextImpl.makeCurrent(GLContextImpl.java:134)
 at com.sun.opengl.impl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:182)
 at javax.media.opengl.GLCanvas.maybeDoSingleThreadedWorkaround(GLCanvas.java:412)
 at javax.media.opengl.GLCanvas.display(GLCanvas.java:244)
 at javax.media.opengl.GLCanvas.paint(GLCanvas.java:277)
 at sun.awt.RepaintArea.paintComponent(RepaintArea.java:276)
 at sun.awt.RepaintArea.paint(RepaintArea.java:241)
 at apple.awt.ComponentModel.handleEvent(ComponentModel.java:263)
 at java.awt.Component.dispatchEventImpl(Component.java:4812)
 at java.awt.Component.dispatchEvent(Component.java:4566)
 at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680)
 at java.awt.EventQueue.access$000(EventQueue.java:86)
 at java.awt.EventQueue$1.run(EventQueue.java:639)
 at java.awt.EventQueue$1.run(EventQueue.java:637)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
 at java.awt.EventQueue$2.run(EventQueue.java:653)
 at java.awt.EventQueue$2.run(EventQueue.java:651)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)
 at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:148)
[catch] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
 at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
 at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Diagnostic information
Input arguments:
 -Djdk.home=/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
 -Dnetbeans.system_http_proxy=DIRECT
 -Dnetbeans.system_http_non_proxy_hosts=
 -Dnetbeans.dirs=/Applications/gephi.app/Contents/MacOS/../Resources/gephi/bin/../gephi:
 -Dnetbeans.home=/Applications/gephi.app/Contents/Resources/gephi/platform
 -Dcom.apple.mrj.application.apple.menu.about.name=gephi
 -Xms64m
 -Xmx1400m
 -Dsun.java2d.noddraw=true
 -Dsun.awt.noerasebackground=false
 -Duser.language=en
 -XX:+HeapDumpOnOutOfMemoryError
 -XX:HeapDumpPath=/Users/stefanicrabtree/Library/Application
 Support/gephi/dev/var/log/heapdump.hprof
Compiler: HotSpot 64-Bit Server Compiler
Heap memory usage: initial 64.0MB maximum 1395.9MB
Non heap memory usage: initial 23.2MB maximum 130.0MB
Garbage collector: ParNew (Collections=5 Total time spent=0s)
Garbage collector: ConcurrentMarkSweep (Collections=4 Total time spent=0s)
Classes: loaded=5559 total loaded=5559 unloaded 0
INFO [org.netbeans.core.ui.warmup.DiagnosticTask]: Total memory 2,147,483,648
INFO [null]: Total physical memory 2,147,483,648
setWindowAlpha(): To avoid content dragging, setWindowAlpha() must be called before the window is realized, or apple.awt.draggableWindowBackground must be set to Boolean.FALSE before the window is realized. If you really want content dragging, set apple.awt.draggableWindowBackground on the window's root pane to Boolean.TRUE before calling setWindowAlpha() to hide this message.
WARNING [org.openide.filesystems.Ordering]: Not all children in Menu/Window/ marked with the position attribute: [TimelineAction.shadow], but some are: [ClusteringAction.shadow, ContextAction.shadow, DataTableAction.shadow, org-netbeans-modules-favorites-View.shadow, FiltersAction.shadow, GraphAction.shadow, HierarchyAction.shadow, LayoutAction.shadow, PartitionAction.shadow, PreviewAction.shadow, PreviewSettingsAction.shadow, RankingAction.shadow, StatisticsAction.shadow, WelcomeAction.shadow, Separator3.instance, CloseWindowAction.shadow, MaximizeWindowAction.shadow, org-netbeans-core-windows-actions-UndockAction.shadow, Separator4.instance, Separator4_1.instance]
# Nodes loaded: 34
# Edges loaded: 78
SEVERE [global]
javax.media.opengl.GLException: Attempt to make the same context current twice on thread Thread[AWT-EventQueue-1,6,IDE Main]
 at com.sun.opengl.impl.GLContextLock.lock(GLContextLock.java:83)
 at com.sun.opengl.impl.GLContextImpl.makeCurrent(GLContextImpl.java:131)
 at com.sun.opengl.impl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:182)
 at javax.media.opengl.GLCanvas.maybeDoSingleThreadedWorkaround(GLCanvas.java:412)
 at javax.media.opengl.GLCanvas.display(GLCanvas.java:244)
 at javax.media.opengl.GLCanvas.paint(GLCanvas.java:277)
 at sun.awt.RepaintArea.paintComponent(RepaintArea.java:276)
 at sun.awt.RepaintArea.paint(RepaintArea.java:241)
 at apple.awt.ComponentModel.handleEvent(ComponentModel.java:263)
 at java.awt.Component.dispatchEventImpl(Component.java:4812)
 at java.awt.Component.dispatchEvent(Component.java:4566)
 at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680)
 at java.awt.EventQueue.access$000(EventQueue.java:86)
 at java.awt.EventQueue$1.run(EventQueue.java:639)
 at java.awt.EventQueue$1.run(EventQueue.java:637)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
 at java.awt.EventQueue$2.run(EventQueue.java:653)
 at java.awt.EventQueue$2.run(EventQueue.java:651)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)
 at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:148)
[catch] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
 at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
 at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
SEVERE [global]
javax.media.opengl.GLException: Attempt to make the same context current twice on thread Thread[AWT-EventQueue-1,6,IDE Main]
 at com.sun.opengl.impl.GLContextLock.lock(GLContextLock.java:83)
 at com.sun.opengl.impl.GLContextImpl.makeCurrent(GLContextImpl.java:131)
 at com.sun.opengl.impl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:182)
 at javax.media.opengl.GLCanvas.maybeDoSingleThreadedWorkaround(GLCanvas.java:412)
 at javax.media.opengl.GLCanvas.display(GLCanvas.java:244)
 at javax.media.opengl.GLCanvas.paint(GLCanvas.java:277)
 at sun.awt.RepaintArea.paintComponent(RepaintArea.java:276)
 at sun.awt.RepaintArea.paint(RepaintArea.java:241)
 at apple.awt.ComponentModel.handleEvent(ComponentModel.java:263)
 at java.awt.Component.dispatchEventImpl(Component.java:4812)
 at java.awt.Component.dispatchEvent(Component.java:4566)
 at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680)
 at java.awt.EventQueue.access$000(EventQueue.java:86)
 at java.awt.EventQueue$1.run(EventQueue.java:639)
 at java.awt.EventQueue$1.run(EventQueue.java:637)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
 at java.awt.EventQueue$2.run(EventQueue.java:653)
 at java.awt.EventQueue$2.run(EventQueue.java:651)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)
 at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:148)
[catch] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
 at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
 at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
SEVERE [global]
javax.media.opengl.GLException: Attempt to make the same context current twice on thread Thread[AWT-EventQueue-1,6,IDE Main]
 at com.sun.opengl.impl.GLContextLock.lock(GLContextLock.java:83)
 at com.sun.opengl.impl.GLContextImpl.makeCurrent(GLContextImpl.java:131)
 at com.sun.opengl.impl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:182)
 at javax.media.opengl.GLCanvas.maybeDoSingleThreadedWorkaround(GLCanvas.java:412)
 at javax.media.opengl.GLCanvas.display(GLCanvas.java:244)
 at javax.media.opengl.GLCanvas.paint(GLCanvas.java:277)
 at sun.awt.RepaintArea.paintComponent(RepaintArea.java:276)
 at sun.awt.RepaintArea.paint(RepaintArea.java:241)
 at apple.awt.ComponentModel.handleEvent(ComponentModel.java:263)
 at java.awt.Component.dispatchEventImpl(Component.java:4812)
 at java.awt.Component.dispatchEvent(Component.java:4566)
 at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680)
 at java.awt.EventQueue.access$000(EventQueue.java:86)
 at java.awt.EventQueue$1.run(EventQueue.java:639)
 at java.awt.EventQueue$1.run(EventQueue.java:637)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
 at java.awt.EventQueue$2.run(EventQueue.java:653)
 at java.awt.EventQueue$2.run(EventQueue.java:651)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)
 at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:148)
[catch] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
 at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
 at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
SEVERE [global]
javax.media.opengl.GLException: Attempt to make the same context current twice on thread Thread[AWT-EventQueue-1,6,IDE Main]
 at com.sun.opengl.impl.GLContextLock.lock(GLContextLock.java:83)
 at com.sun.opengl.impl.GLContextImpl.makeCurrent(GLContextImpl.java:131)
 at com.sun.opengl.impl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:182)
 at javax.media.opengl.GLCanvas.maybeDoSingleThreadedWorkaround(GLCanvas.java:412)
 at javax.media.opengl.GLCanvas.display(GLCanvas.java:244)
 at javax.media.opengl.GLCanvas.paint(GLCanvas.java:277)
 at sun.awt.RepaintArea.paintComponent(RepaintArea.java:276)
 at sun.awt.RepaintArea.paint(RepaintArea.java:241)
 at apple.awt.ComponentModel.handleEvent(ComponentModel.java:263)
 at java.awt.Component.dispatchEventImpl(Component.java:4812)
 at java.awt.Component.dispatchEvent(Component.java:4566)
 at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680)
 at java.awt.EventQueue.access$000(EventQueue.java:86)
 at java.awt.EventQueue$1.run(EventQueue.java:639)
 at java.awt.EventQueue$1.run(EventQueue.java:637)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
 at java.awt.EventQueue$2.run(EventQueue.java:653)
 at java.awt.EventQueue$2.run(EventQueue.java:651)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)
 at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:148)
[catch] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
 at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
 at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
WARNING [org.netbeans.modules.autoupdate.updateproviders.AutoupdateCatalogFactory]: Services/AutoupdateType/org_gephi_branding_desktop_update_center.instance: url_key attribute deprecated in favor of url
WARNING [org.netbeans.modules.autoupdate.updateproviders.AutoupdateCatalogFactory]: Services/AutoupdateType/org_gephi_branding_desktop_update_center_1.instance: url_key attribute deprecated in favor of url

Revision history for this message
Mathieu Bastian (mathieu.bastian) said : 		#3

It looks like there is a jogl.jar in the JDK extensions:

/Library/Java/Extensions/jogl.jar

Could you please try to delete (or move it temporarily elsewhere) this file and try again It should solve the problem.

Revision history for this message
Stefani Crabtree (stefanicrabtree) said : 		#4

This did not help. Is there another idea?

-Stefani

On Sun, Jun 19, 2011 at 11:51 AM, Mathieu Bastian <
<email address hidden>> wrote:

> Your question #161538 on Gephi changed:
> https://answers.launchpad.net/gephi/+question/161538
>
> Status: Open => Answered
>
> Mathieu Bastian proposed the following answer:
> It looks like there is a jogl.jar in the JDK extensions:
>
> /Library/Java/Extensions/jogl.jar
>
> Could you please try to delete (or move it temporarily elsewhere) this
> file and try again It should solve the problem.
>
> --
> If this answers your question, please go to the following page to let us
> know that it is solved:
> https://answers.launchpad.net/gephi/+question/161538/+confirm?answer_id=2
>
> If you still need help, you can reply to this email or go to the
> following page to enter your feedback:
> https://answers.launchpad.net/gephi/+question/161538
>
> You received this question notification because you asked the question.
>

--
M.A. Candidate
Archaeology
Washington State University

Life is short and research is long.
-Gerald Holton

Revision history for this message
Mathieu Bastian (mathieu.bastian) said : 		#5

Ok, I forgot to mention

/Library/Java/Extensions/gluegen-rt.jar

is going with JOGL, so you may do the same operation with this one

Revision history for this message
Stefani Crabtree (stefanicrabtree) said : 		#6

Didn't work. I'm attaching screen shots of some new errors and the spinning
ball of doom.

On Tue, Jun 21, 2011 at 4:45 PM, Mathieu Bastian <
<email address hidden>> wrote:

> Your question #161538 on Gephi changed:
> https://answers.launchpad.net/gephi/+question/161538
>
> Status: Open => Answered
>
> Mathieu Bastian proposed the following answer:
> Ok, I forgot to mention
>
> /Library/Java/Extensions/gluegen-rt.jar
>
> is going with JOGL, so you may do the same operation with this one
>
> --
> If this answers your question, please go to the following page to let us
> know that it is solved:
> https://answers.launchpad.net/gephi/+question/161538/+confirm?answer_id=4
>
> If you still need help, you can reply to this email or go to the
> following page to enter your feedback:
> https://answers.launchpad.net/gephi/+question/161538
>
> You received this question notification because you asked the question.
>

--
M.A. Candidate
Archaeology
Washington State University

Life is short and research is long.
-Gerald Holton

Revision history for this message
Mathieu Bastian (mathieu.bastian) said : 		#7

Could you please attach the errors you get? Thank you

Can you help with this problem?

Provide an answer of your own, or ask Stefani Crabtree for more information if necessary.

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