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Gephi isn't compatible with Java 7 and 8 on all platforms (Windows, Mac OS X, Linux) #748

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kikohs opened this issue Feb 20, 2013 · 65 comments
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@kikohs
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@kikohs kikohs commented Feb 20, 2013

Hello,

I have cleaned the user folder and downloaded a fresh copy of gephi. I can't open any graph even the examples. The visualization is broken.

I even update java to the latest patches.

Help

Log Session: Wednesday, February 20, 2013 3:41:18 PM CET
System Info:
Product Version = Gephi 0.8.2 201210100934
Operating System = Mac OS X version 10.8.2 running on x86_64
Java; VM; Vendor = 1.7.0_15; Java HotSpot(TM) 64-Bit Server VM 23.7-b01; Oracle Corporation
Runtime = Java(TM) SE Runtime Environment 1.7.0_15-b03
Java Home = /Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre
System Locale; Encoding = en_US (gephi); US-ASCII
Home Directory = /Users/kikohs
Current Directory = /
User Directory = /Users/kikohs/Library/Application Support/gephi/0.8.2/dev
Cache Directory = /Users/kikohs/Library/Application Support/gephi/0.8.2/dev/var/cache
Installation = /Volumes/Gephi/Gephi.app/Contents/Resources/gephi/gephi
/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform
/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform
Boot & Ext. Classpath = /Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre/lib/resources.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre/lib/rt.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre/lib/sunrsasign.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre/lib/jsse.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre/lib/jce.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre/lib/charsets.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre/lib/jfr.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre/lib/JObjC.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre/classes:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre/lib/ext/dnsns.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre/lib/ext/localedata.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre/lib/ext/sunec.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre/lib/ext/sunjce_provider.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre/lib/ext/sunpkcs11.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/jre/lib/ext/zipfs.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
Application Classpath = /Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/boot.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/org-openide-modules.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/org-openide-util-lookup.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/org-openide-util.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ar_SA.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_bg.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ca.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_cs.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_de.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_es.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_fr.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_gl_ES.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_in_ID.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_it.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ja.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ko.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_nl_NL.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_pl.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_pt_BR.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_pt_PT.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ro.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ru.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_si.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_sq.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_sv.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_tr.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_zh_CN.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_zh_TW.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ar_SA.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_bg.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ca.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_cs.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_de.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_es.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_fr.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_gl_ES.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_in_ID.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_it.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ja.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ko.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_nl_NL.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_pl.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_pt_BR.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_pt_PT.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ro.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ru.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_si.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_sq.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_sv.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_tr.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_zh_CN.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_zh_TW.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_bg.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ca.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_cs.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_de.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_es.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_fr.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_gl_ES.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_in_ID.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_it.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ja.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ko.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_nl_NL.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_pl.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_pt_BR.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ro.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ru.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_si.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_sv.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_tr.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_zh_CN.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ar_SA.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_bg.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ca.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_cs.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_de.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_es.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_fr.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_gl_ES.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_in_ID.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_it.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ja.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ko.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_nl_NL.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_pl.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_pt_BR.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_pt_PT.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ro.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ru.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_si.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_sq.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_sv.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_tr.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_zh_CN.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_zh_TW.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/lib/dt.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_15.jdk/Contents/Home/lib/tools.jar

Startup Classpath = /Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/core.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/org-openide-filesystems.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_ar_SA.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_bg.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_ca.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_cs.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_de.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_es.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_fr.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_gl_ES.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_in_ID.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_it.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_ja.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_ko.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_nl_NL.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_pl.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_pt_BR.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_pt_PT.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_ro.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_ru.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_si.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_sq.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_sv.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_tr.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_zh_CN.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_zh_TW.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ar_SA.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_bg.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ca.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_cs.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_de.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_es.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_fr.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_gl_ES.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_in_ID.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_it.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ja.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ko.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_nl_NL.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_pl.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_pt_BR.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_pt_PT.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ro.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ru.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_si.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_sq.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_sv.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_tr.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_zh_CN.jar:/Volumes/Gephi/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_zh_TW.jar:/Volumes/Gephi/Gephi.app/Contents/MacOS/../Resources/gephi/bin/../gephi/core/locale/core_gephi.jar

WARNING [org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings]: The property "netbeans.default_userdir_root" was not set!
SEVERE [org.netbeans.core.modules]
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:722)
INFO [org.netbeans.core.startup.NbEvents]: Turning on modules:
org.openide.util.lookup [8.15.2 201210100934]
org.openide.util [8.25.2 201210100934]
org.openide.modules [7.32.1 201210100934]
org.openide.filesystems [7.62.1 201210100934]
org.netbeans.api.annotations.common/1 [1.14.1 201210100934]
org.openide.awt [7.46.1 201210100934]
org.netbeans.api.progress/1 [1.28.1 201210100934]
org.openide.dialogs [7.25.1 201210100934]
org.openide.nodes [7.28.1 201210100934]
org.openide.windows [6.55.2 201210100934]
org.netbeans.modules.editor.mimelookup/1 [1.26.1 201210100934]
org.openide.text [6.49.3 201210100934]
org.netbeans.swing.tabcontrol [1.36.1 201210100934]
org.netbeans.swing.outline [1.20.1 201210100934]
org.openide.explorer [6.45.1 201210100934]
org.openide.actions [6.26.1 201210100934]
org.netbeans.modules.queries/1 [1.28.1 201210100934]
org.openide.loaders [7.37.3 201210100934]
org.openide.io [1.31.2 201210100934]
org.netbeans.swing.plaf [1.25.1 201210100934]
org.netbeans.spi.quicksearch [1.14.1 201210100934]
org.netbeans.bootstrap/1 [2.52.3 201210100934]
org.netbeans.core.startup/1 [1.40.1 201210100934]
org.netbeans.modules.settings/1 [1.35.1 201210100934]
org.netbeans.modules.sendopts/2 [2.22.1 201210100934]
org.netbeans.modules.sampler [1.1.1 201210100934]
org.netbeans.modules.progress.ui [1.20.1 201210100934]
org.netbeans.modules.print [7.13.1 201210100934]
org.netbeans.modules.keyring [1.11.1 201210100934]
org.netbeans.core/2 [3.33.1 201210100934]
org.netbeans.modules.options.api/1 [1.26.1 201210100934]
org.netbeans.modules.options.keymap [1.19.2 201210100934]
org.netbeans.modules.masterfs/2 [2.38.2 201210100934]
org.netbeans.libs.jna/1 [1.21.1 201210100934]
org.netbeans.modules.masterfs.macosx [1.1.1 201210100934]
org.netbeans.modules.keyring.impl [1.7.1 201210100934]
org.netbeans.modules.favorites/1 [1.29.1 201210100934]
org.netbeans.modules.editor.mimelookup.impl/1 [1.18.1 201210100934]
org.netbeans.modules.autoupdate.services [1.33.2 201210100934]
org.netbeans.core.ui/1 [1.31.1 201210100934]
org.netbeans.modules.autoupdate.ui [1.27.3 201210100934]
org.netbeans.libs.osgi [1.9.1 201210100934]
org.netbeans.libs.felix [2.3.1 201210100934]
org.netbeans.core.windows/2 [2.49.3 201210100934]
org.netbeans.modules.core.kit [1.16.1 201210100934]
org.netbeans.modules.applemenu/1 [1.24.1 201210100934]
org.netbeans.core.output2/1 [1.26.1 201210100934]
org.netbeans.core.netigso [1.16.1 201210100934]
org.netbeans.core.nativeaccess/1 [1.16.1 201210100934]
org.netbeans.core.io.ui/1 [1.16.1 201210100934]
org.gephi.utils.longtask [0.8.2 0.8.2 201301030113]
org.gephi.project.api [0.8.2 0.8.2 201301030113]
org.gephi.core.library.wrapper [0.8.2 0.8.2 201301030114]
org.gephi.utils [0.8.2 0.8.2 201301030114]
org.gephi.graph.api [0.8.2 0.8.2 201301030114]
org.gephi.data.attributes.api [0.8.2 0.8.2 201301030114]
org.gephi.lib.validation [0.8.2 0.8.2 201301030114]
org.gephi.ui.utils [0.8.2 0.8.2 201301030115]
org.gephi.ui.library.wrapper [0.8.2 0.8.2 201301030114]
org.gephi.ui.components [0.8.2 0.8.2 201301030115]
org.gephi.workspace.ui [0.8.2 0.8.2 201301030117]
org.gephi.db.drivers [0.8.2 0.8.2 201301030115]
org.gephi.dynamic.api [0.8.2 0.8.2 201301030114]
org.gephi.io.importer.api [0.8.2 0.8.2 201301030115]
org.gephi.mostrecentfiles.api [0.8.2 0.8.2 201301030117]
org.gephi.desktop.project [0.8.2 0.8.2 201301030117]
org.gephi.welcome.screen [0.8.2 0.8.2 201301030117]
org.gephi.datalab.api [0.8.2 0.8.2 201301030114]
org.gephi.visualization.api [0.8.2 0.8.2 201301030115]
org.gephi.tools.api [0.8.2 0.8.2 201301030116]
org.gephi.utils.collection [0.8.2 0.8.2 201301030117]
org.gephi.gleem [0.8.2 0.8.2 201301030117]
org.gephi.visualization [0.8.2 0.8.2 201301030117]
org.gephi.ui.propertyeditor [0.8.2 0.8.2 201301030119]
org.gephi.algorithms.plugin [0.8.2 0.8.2 201301030116]
org.gephi.tools.plugin [0.8.2 0.8.2 201301030117]
org.gephi.timeline [0.8.2 0.8.2 201301030116]
org.gephi.statistics.api [0.8.2 0.8.2 201301030116]
org.gephi.statistics.plugin [0.8.2 0.8.2 201301030116]
org.gephi.statistics.plugin.ui [0.8.2 0.8.2 201301030116]
org.gephi.ranking.api [0.8.2 0.8.2 201301030115]
org.gephi.spline.editor [0.8.2 0.8.2 201301030116]
org.gephi.spigot.plugin [0.8.2 0.8.2 201301030116]
org.gephi.spigot.plugin.ui [0.8.2 0.8.2 201301030116]
org.gephi.settings.upgrader [0.8.2 0.8.2 201301030116]
org.gephi.ranking.plugin [0.8.2 0.8.2 201301030115]
org.gephi.ranking.plugin.ui [0.8.2 0.8.2 201301030116]
org.gephi.project.ui [0.8.2 0.8.2 201301030115]
org.gephi.io.processor.plugin [0.8.2 0.8.2 201301030115]
org.gephi.processor.plugin.ui [0.8.2 0.8.2 201301030115]
org.gephi.preview.api [0.8.2 0.8.2 201301030114]
org.gephi.preview.plugin [0.8.2 0.8.2 201301030115]
org.gephi.io.exporter.api [0.8.2 0.8.2 201301030113]
org.gephi.io.exporter.preview [0.8.2 0.8.2 201301030114]
org.gephi.preview.export.ui [0.8.2 0.8.2 201301030114]
org.gephi.perspective.api [0.8.2 0.8.2 201301030120]
org.gephi.partition.api [0.8.2 0.8.2 201301030119]
org.gephi.partition.plugin [0.8.2 0.8.2 201301030121]
org.gephi.partition.plugin.ui [0.8.2 0.8.2 201301030121]
org.gephi.layout.api [0.8.2 0.8.2 201301030118]
org.gephi.layout.plugin [0.8.2 0.8.2 201301030119]
org.gephi.io.importer.plugin [0.8.2 0.8.2 201301030119]
org.gephi.io.generator.api [0.8.2 0.8.2 201301030118]
org.gephi.io.generator.plugin [0.8.2 0.8.2 201301030118]
org.gephi.io.exporter.plugin [0.8.2 0.8.2 201301030118]
org.gephi.import.plugin.ui [0.8.2 0.8.2 201301030120]
org.gephi.graph.dhns [0.8.2 0.8.2 201301030119]
org.gephi.gephi.branding [0.8.2 0.8.2 201301030113]
org.gephi.generator.plugin.ui [0.8.2 0.8.2 201301030118]
org.gephi.filters.api [0.8.2 0.8.2 201301030118]
org.gephi.filters.plugin [0.8.2 0.8.2 201301030120]
org.gephi.desktop.perspective [0.8.2 0.8.2 201301030120]
org.gephi.filters.plugin.ui [0.8.2 0.8.2 201301030121]
org.gephi.filters.impl [0.8.2 0.8.2 201301030120]
org.gephi.export.plugin.ui [0.8.2 0.8.2 201301030120]
org.gephi.dynamic.impl [0.8.2 0.8.2 201301030121]
org.gephi.directory.chooser [0.8.2 0.8.2 201301030122]
org.gephi.desktop.tools [0.8.2 0.8.2 201301030121]
org.gephi.desktop.timeline [0.8.2 0.8.2 201301030122]
org.gephi.desktop.statistics [0.8.2 0.8.2 201301030118]
org.gephi.desktop.spigot [0.8.2 0.8.2 201301030119]
org.gephi.desktop.recent.files [0.8.2 0.8.2 201301030120]
org.gephi.desktop.ranking [0.8.2 0.8.2 201301030118]
org.gephi.desktop.progress [0.8.2 0.8.2 201301030118]
org.gephi.desktop.io.export [0.8.2 0.8.2 201301030120]
org.gephi.desktop.preview [0.8.2 0.8.2 201301030121]
org.gephi.desktop.partition [0.8.2 0.8.2 201301030119]
org.gephi.desktop.layout [0.8.2 0.8.2 201301030121]
org.gephi.desktop.import [0.8.2 0.8.2 201301030121]
org.gephi.desktop.hierarchy [0.8.2 0.8.2 201301030120]
org.gephi.desktop.generate [0.8.2 0.8.2 201301030119]
org.gephi.desktop.filters [0.8.2 0.8.2 201301030122]
org.gephi.desktop.datalab [0.8.2 0.8.2 201301030119]
org.gephi.desktop.context [0.8.2 0.8.2 201301030117]
org.gephi.clustering.api [0.8.2 0.8.2 201301030118]
org.gephi.desktop.clustering [0.8.2 0.8.2 201301030120]
org.gephi.desktop.branding [0.8.2 0.8.2 201301030118]
org.gephi.datalab.plugin [0.8.2 0.8.2 201301030121]
org.gephi.clustering.plugin [0.8.2 0.8.2 201301030122]
org.gephi.attributes [0.8.2 0.8.2 201301030119]
WARNING [org.netbeans.TopSecurityManager]: use of system property netbeans.user has been obsoleted in favor of InstalledFileLocator/Places at org.gephi.ui.upgrader.Upgrader.getCurrentVersion(Upgrader.java:123)
SEVERE [global]
java.lang.ClassNotFoundException: apple.awt.ComponentModel
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
at org.netbeans.ProxyClassLoader.loadClass(ProxyClassLoader.java:262)
Caused: java.lang.ClassNotFoundException: apple.awt.ComponentModel starting from ModuleCL@5f679f6[org.gephi.visualization] with possible defining loaders null and declared parents [ModuleCL@2ec07b39[org.netbeans.modules.options.api], ModuleCL@7707610f[org.gephi.graph.api], ModuleCL@20e587de[org.gephi.desktop.project], ModuleCL@710ce358[org.gephi.ui.library.wrapper], ModuleCL@593e9bf1[org.gephi.dynamic.api], ModuleCL@3d69b4b9[org.gephi.datalab.api], ModuleCL@2b9f2263[org.netbeans.modules.settings], ModuleCL@6802bf86[org.gephi.project.api], ModuleCL@4af4ba53[org.gephi.ui.utils], ModuleCL@6e2f0bc1[org.gephi.visualization.api], ...10 more]
at org.netbeans.ProxyClassLoader.loadClass(ProxyClassLoader.java:264)
at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
Caused: java.lang.NoClassDefFoundError: apple/awt/ComponentModel
at com.sun.opengl.impl.JAWT_DrawingSurface.GetDrawingSurfaceInfo0(Native Method)
at com.sun.opengl.impl.JAWT_DrawingSurface.GetDrawingSurfaceInfo(JAWT_DrawingSurface.java:56)
at com.sun.opengl.impl.macosx.MacOSXOnscreenGLDrawable$1.run(MacOSXOnscreenGLDrawable.java:165)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.opengl.impl.macosx.MacOSXOnscreenGLDrawable.lockSurface(MacOSXOnscreenGLDrawable.java:163)
at com.sun.opengl.impl.macosx.MacOSXOnscreenGLContext.makeCurrentImpl(MacOSXOnscreenGLContext.java:57)
at com.sun.opengl.impl.GLContextImpl.makeCurrent(GLContextImpl.java:134)
at com.sun.opengl.impl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:182)
at javax.media.opengl.GLCanvas$DisplayOnEventDispatchThreadAction.run(GLCanvas.java:452)
at sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run(OGLRenderQueue.java:234)
Caused: javax.media.opengl.GLException
at com.sun.opengl.impl.Java2D.invokeWithOGLContextCurrent(Java2D.java:296)
at javax.media.opengl.Threading.invokeOnOpenGLThread(Threading.java:266)
at javax.media.opengl.GLCanvas.maybeDoSingleThreadedWorkaround(GLCanvas.java:410)
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:264)
at sun.lwawt.LWRepaintArea.paintComponent(LWRepaintArea.java:54)
at sun.awt.RepaintArea.paint(RepaintArea.java:240)
at sun.lwawt.LWComponentPeer.handleJavaPaintEvent(LWComponentPeer.java:1277)
at sun.lwawt.LWComponentPeer.handleEvent(LWComponentPeer.java:1165)
at java.awt.Component.dispatchEventImpl(Component.java:4937)
at java.awt.Component.dispatchEvent(Component.java:4687)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:729)
at java.awt.EventQueue.access$200(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:688)
at java.awt.EventQueue$3.run(EventQueue.java:686)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
at java.awt.EventQueue$4.run(EventQueue.java:702)
at java.awt.EventQueue$4.run(EventQueue.java:700)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:699)
at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:158)
[catch] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

@eduramiba
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@eduramiba eduramiba commented Feb 20, 2013

This seems to be a problem happening with JOGL 1.1 in Java 7 for Mac OS

@kikohs
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@kikohs kikohs commented Feb 20, 2013

It is fixable ?

@eduramiba
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@eduramiba eduramiba commented Feb 20, 2013

This would be probably fixed by switching to JOGL 2, but that is not an inmediate process, and could bring new problems.

I found a bug that is similar to this issue, but they advice to solve this by a downgrade to java 6 http://forum.salemthegame.com/viewtopic.php?f=10&t=1645

@kikohs
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@kikohs kikohs commented Feb 20, 2013

I am a scala developer, I cannot switch back to java 6. This is very annoying, hope you guys fix this issue ASAP as it virtually breaks Gephi on any mac. With the recent Java security issues, it is more than strongly recommended to install the latest patches from Oracle.

@andykitchen
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@andykitchen andykitchen commented Mar 6, 2013

Bump, this is also broken for me too. You can work around this by opening the nbexec file inside
gephi and changing the lines:

        Darwin*)
        # read Java Preferences
        if [ -x "/usr/libexec/java_home" ]; then
            jdkhome=`/usr/libexec/java_home`

to

        Darwin*)
        # read Java Preferences
        if [ -x "/usr/libexec/java_home" ]; then
            jdkhome=`/usr/libexec/java_home -v 1.6\*`

It's ugly but it works.

@jbilcke
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@jbilcke jbilcke commented Mar 7, 2013

@kikohs I'm afraid it will take some time for Gephi to migrate to JOGL 2.

I'm too stuck with this JDK7/JOGL issue..

@jbilcke
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@jbilcke jbilcke commented Mar 7, 2013

I'm trying to port/hack Gephi to use JOGL2, in compatibility mode:

MfgLabs/gephi-mfg-plugins@master...jogl2

it does compile but still fails to load the libraries, not surprising I'm probably doing it wrong.

@ghost ghost assigned mbastian Mar 7, 2013
@andykitchen
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@andykitchen andykitchen commented Mar 8, 2013

@jbilcke I've tested your fork, it works for me! You need to use Java 1.6 though...

$ cd modules/application
# Run using apple java 1.6
$ JAVA_HOME=/Library/Java/Home mvn nbm:cluster-app nbm:run-platform

This also means that the java 7 problem is more complicated
than just having an old version of JOGL.

@andykitchen
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@andykitchen andykitchen commented Mar 8, 2013

ugh, no sorry that was incorrect I accidentally forgot to rebuild after I switched branches. Although this means origin/master works so long as one launches it with the correct JAVA_HOME path.

@jbilcke
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@jbilcke jbilcke commented Mar 8, 2013

Yes the "/usr/libexec/java_home -v 1.6" does the trick (fortunately installing JDK7 does not remove the Apple-provided JDK6)

@mbastian
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@mbastian mbastian commented Mar 8, 2013

We should probably investigate in creating a Gephi version which embeds the JRE until this is resolved.

@mbastian
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@mbastian mbastian commented Mar 8, 2013

@jbilcke You may want to look how Antonio was made JOGL2 work in his branch at the time he was working on the new vizengine: https://github.com/gephi/gephi/tree/new-vizengine/JogAmp%20Wrapper

The natives librairies don't need to be manually loaded using the "JOGLNativesInstaller" class so you may also want to remove/disable this file.

@sbourke
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@sbourke sbourke commented Mar 21, 2013

Just another moaner from the internet who was also having a same problem. I'm not proposing any solutions or doing anything constructive :-)

@mbastian
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@mbastian mbastian commented Apr 16, 2013

I'm working on resolving this issue but it will need some time to migrate to JOGL2. After investigation there are not really another solution. Stay tuned.

@simonwibberley
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@simonwibberley simonwibberley commented Jun 11, 2013

A hack that worked for me is to hard code the 1.6 java home into the Gephi run script:
add

jdkhome="`/usr/libexec/java_home -v 1.6`"

at around line 50 to:
/Applications/Gephi.app/Contents/MacOS/Gephi
hth

@jnankivel
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@jnankivel jnankivel commented Jul 26, 2013

I'd really love to try out gephi, but I've had the issue referenced here on 2 different Macs and have never gotten it to run. :-(

@bgriffen
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@bgriffen bgriffen commented Jul 30, 2013

Has any progress been made on this bug? I can't find a way to downgrade to Java 6 as 10.7.5 has removed the Java Utilities from Applications/Utilities/. I've been searching for work arounds for hours and have given up. I have a bunch of project I'd like to explore on Gephi but can't do anything at the moment. A bunch of friends have the same issue. :(

@mbastian
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@mbastian mbastian commented Jul 31, 2013

You should still have Java6 on your Mac and the trick is just to tell to Gephi to use it instead of the default Java7:

  1. Edit file /Applications/Gephi.app/Contents/Resources/gephi/etc/gephi.conf
  2. Set the jdkhome parameter to the location of Java6
  3. Save the file and try to start Gephi again

This is how it looks like for me:

#default location of JDK/JRE, can be overridden by using --jdkhome <dir> switch
jdkhome="/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/"

On the bug, I have a working version that fixes the problem but it's not ready for release yet.

@bgriffen
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@bgriffen bgriffen commented Jul 31, 2013

Thanks very much.
Brendan

On Wed, Jul 31, 2013 at 2:27 AM, Mathieu Bastian
notifications@github.comwrote:

You should still have Java6 on your Mac and the trick is just to tell to
Gephi to use it instead of the default Java7:

  1. Edit file
    /Applications/Gephi.app/Contents/Resources/gephi/etc/gephi.conf
  2. Set the jdkhome parameter to the location of Java6
  3. Save the file and try to start Gephi again

This is how it looks like for me:
default location of JDK/JRE, can be overridden by using --jdkhome switch

jdkhome="/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/"

On the bug, I have a working version that fixes the problem but it's not
ready for release yet.


Reply to this email directly or view it on GitHubhttps://github.com//issues/748#issuecomment-21842701
.

@Nav270
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@Nav270 Nav270 commented Aug 13, 2013

Thanks to all for the help in this issue; it was incredibly frustrating.

mbastian's method above worked well for me, especially when paired with andykitchen's additional code change further up.

_To any users who are not particularly code-savvy (i.e. me), this will work. Just make sure you have the latest version of the Netbeans IDE (I did not have this...) and if you open the main window of gephi but get just a blank gray screen, go to the plugin's tab on the top and download EVERY SINGLE ONE._

@misterkabir
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@misterkabir misterkabir commented Aug 13, 2013

mbastian's method worked for me as well after installing java 6 through the terminal. Thanks!

@biwa7636
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@biwa7636 biwa7636 commented Sep 4, 2013

frustrating.... still not working for me....

@Nav270
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@Nav270 Nav270 commented Sep 4, 2013

Biwa7636, at what stage of the process are things not working?

@biwa7636
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@biwa7636 biwa7636 commented Sep 4, 2013

It has a blank grey background and with an Unexpected Exception red warning sign on the bottom right. With java.lang.NullPointerException.
According to your previous statements. the plugin's tab doesn't have any new staff you could download. There is no update or plugin to download. (I also have Netbeans IDE installed.)
I looked at the configuration file and see the first line: default_userdir="${HOME}/.${APPNAME}/0.8.2/dev, and I notice there is no folder called '.gephi' under my home directory, do you think it would be a problem?

@bfontaine
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@bfontaine bfontaine commented Oct 8, 2015

FWIW this worked for me on OS X: https://gist.github.com/bfontaine/0dd7f786e274c7139421

@mbastian
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@mbastian mbastian commented Dec 12, 2015

This issue has been fixed and the upcoming 0.9 release will work with Java 7 and 8. It actually will embed the JDK so installing Java won't be necessary anymore. Would appreciate you testing the nightly build https://github.com/gephi/gephi#nightly-builds though so we can resolve potential new Mac OS X issues before the release. Thanks.

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