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

Closed
kikohs opened this Issue Feb 20, 2013 · 65 comments

Projects

None yet
@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@2ec07b3[org.netbeans.modules.options.api], ModuleCL@7707610[org.gephi.graph.api], ModuleCL@20e587d[org.gephi.desktop.project], ModuleCL@710ce35[org.gephi.ui.library.wrapper], ModuleCL@593e9bf[org.gephi.dynamic.api], ModuleCL@3d69b4b[org.gephi.datalab.api], ModuleCL@2b9f226[org.netbeans.modules.settings], ModuleCL@6802bf8[org.gephi.project.api], ModuleCL@4af4ba5[org.gephi.ui.utils], ModuleCL@6e2f0bc[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
Member

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

@kikohs
kikohs commented Feb 20, 2013

It is fixable ?

@eduramiba
Member

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
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

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
Member
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
Member
jbilcke commented Mar 7, 2013

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

MfgLabs@master...jogl2

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

@mbastian mbastian was assigned Mar 7, 2013
@andykitchen

@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

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
Member
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
Member
mbastian commented Mar 8, 2013

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

@mbastian
Member
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
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
Member

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

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

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

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
Member

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

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/gephi/gephi/issues/748#issuecomment-21842701
.

@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

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

@biwa7636
biwa7636 commented Sep 4, 2013

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

@Nav270
Nav270 commented Sep 4, 2013

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

@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?

@Nav270
Nav270 commented Sep 4, 2013

As far as I can tell, I don't have one either and it's working fine. Did you pair mbastians method with the earlier code fix by andykitchen? I did both and it worked, so I guess its possible that mbatians methods when combined with andykitchen's.

Here was his post:


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.


I would scroll up and find it, because the copy and paste tool looks bad for code.

@Nav270
Nav270 commented Sep 4, 2013

Oh never mind, that looks ok. :)

@Nav270
Nav270 commented Sep 4, 2013

This can be found at Gephi>contents>resources>gephi>platform>lib

@berniehogan

Hi all, still getting the nasty "unable to load libjogl_awt.jnilib". I edited the nbexec. I also tested java_home directly to ensure that it would run with 1.6. This happened only recently when I upgraded to 10.8.4 and upgraded java to 7.25. I didn't use gephi between the upgrades so I can't tell which one made a difference. I'm using Gephi 0.8.2. When I use an earlier version the splash screen and error do not even emerge, the program starts and dies.

UPDATE (for anyone else):
I recently reinstalled Mac Mountain Lion. While I did install the latest java update as recommend, it would only be for Java 7. In order to install the correct Java 6 (I had
$java -version
java version "1.6.0_41"
), I had to go to apple and search for it explicitly. It is found here:
http://support.apple.com/kb/DL1572

When I installed this version:
$ java -version
java version "1.6.0_51"

then Gephi worked again.

@rurounijones

Have OSX 10.8.5

Have applied all the code fixes suggested above but no changes unfortunately. Fingers crossed for the next version soon.

(I did not try berniehogan's fix as I do not want to bugger up existing java 7 install in any way 😄 )

@jgieseking

I just went to Java for OS X 2013-004 (http://support.apple.com/kb/DL1572), downloaded Java 6, and installed it. I can open and use Gephi from the .dmg mount. If I copy Gephi to Applications, it partially opens and then just greys out and the drop-downs are empty.

However, when I check the System Prefs --> Java --> Java Control Panel --> Update, it still says Java 7 Update 40 is installed. I turned off Check for Updates Automatically in the same pane hoping that it won't erase the new version.

Horrible workaround but some sort of progress. If I am inane for going back to JDK 6, please let me know.

@ncarboni

You have to uninstall Java 7 first. Follow this instruction
http://docs.oracle.com/javase/7/docs/webnotes/install/mac/mac-jdk.html#uninstall
and then type java -version on the Terminal. You should have 1.6.0_51 :)

@jgieseking

Thanks, WPB!

Also, I figured out how to run Gephi off of my machine rather then through the dmg: follow the install instructions! What a crazy idea!! Per https://gephi.org/users/install/, after the install:
Locate and delete gephi user directory to clean your installation.

On Windows 2K/XP, user diretory is located in C:\Documents and Settings\username\Application Data\.gephi
On Windows Vista/Seven, user directory is located in C:\Users\username\AppData\Roaming\.gephi
On Mac OS X, user directory is located in /Users/username/Library/Application Support/gephi
On Linux, user diretory is located in /home/username/.gephi

Cheers.

@brianmingus

Gephi is broken on OSX 10.8.5. I tried every fix in this thread except for downgrading java, which is obviously not a solution that should be recommended to users.

@jbilcke
Member
jbilcke commented Oct 21, 2013

You do not have java6 in /System/Library/Java/JavaVirtualMachines/ ?

@jgieseking

I spoke to some Java experts and what you need to do is install Java 6 on your machine from the link I noted previously [Java for OS X 2013-004 (http://support.apple.com/kb/DL1572)], and then go to System Preferences-->Java and update back to Java 7. The issue isn't one version or another, but rather that new Macs do not come with Java 6 packaged in under Java 7. Java 7 is a whole new beast. So once you put in Java 6 and turn back to 7, Gephi can still find Java 6 and continue to work. I did this on my home machine (after much angst) and then my work machine and they are both working great.

@rurounijones

People on this issue might be interested in this commit: 7409c4f which (by the looks of it) might fix this issue.

I would guess giving the nightly build a go might be good. (Remember that it is not a stable build so it might not work, but you can at least see if the library issue is fixed for you.)

@eduramiba - Could you comment?

@jgieseking

That is so wacky, wendellpboyd. Works for me. Maybe a IP/location issue? Here's the link to the Java 6 download file from that site: http://support.apple.com/downloads/DL1572/en_US/JavaForOSX2013-05.dmg

@immcpeak

I had the problem and solved it as suggested above:

  1. Install Java 7 on OS X Maverick
  2. Install Java 6
  3. Install Gephi

Works

@aarellano

To run Gephi on OS X Mavericks, just install the Apple's update for Java 6 http://support.apple.com/kb/DL1572?viewlocale=en_US

If you still have problems it probably means that you have Java 7 installed, and Gephi is using it. You can override that behavior by editing Gephi's config file:
open /Applications/Gephi.app/Contents/Resources/gephi/etc/gephi.conf and set the jdkhome value to:
jdkhome="/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home"

@metasim
metasim commented Nov 27, 2013

As a point of reference, the Java bindings to VTK (another OpenGL based visualization toolkit) and other OpenGL bindings broke with the Oracle version of Java 7. Has something to do with not having an "NSView-based implementation of sun.awt.EmbeddedFrame". There's a possibility that build 40 of Java 7 may have fixed this, but I haven't confirmed. The options above to force running under Java 6 should work, but should you require Java 7, know that the problem isn't limited to Gephi.

Some potentially relevant links:

@metasim
metasim commented Nov 27, 2013

PS: You can confirm whether or not the changes above were accepted by going to gephi -> About... and checking the Java version, as shown below:

screen shot 2013-11-27 at 12 28 20 pm

I had to set the javahome variable above the existence test to get it to work on my machine (MacOS X 10.9).

screen shot 2013-11-27 at 12 29 33 pm

@rezmont
rezmont commented Dec 5, 2013

Hi all,

It seems that this problem is there for all Mac users. I am using gephi on my Ubuntu box at work, but I can get it to run on my MacBook at home. I did install the the Apple's update for Java 6 (http://support.apple.com/kb/DL1572?viewlocale=en_US) recommended by aarellano.

I also reset the confing file in:
/Applications/Gephi.app/Contents/Resources/gephi/etc/gephi.conf
I added the following line:
jdkhome="/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home"

I also did the check suggested by metasim to see which java my gephi is using and the output shows I am using the right version of java:
Product Version: Gephi 0.8.2 201210100934
Java: 1.6.0_65; Java HotSpot(TM) 64-Bit Server VM 20.65-b04-462
System: Mac OS X version 10.9 running on x86_64; MacRoman; en_US (gephi)

I still can not open graph files that I can open on my ubuntu box. I receive the NullPointerException.

Can an expert who has actually fixed the problem enumerate the things that I should do to fix my installation of gephi. Thank you.

@kikohs
kikohs commented Dec 5, 2013

The trick that worked for me is to completely uninstall Gephi using AppCleaner (free software). Once you've removed all the files but the .app. it worked as expected.

Moreover, in your .bash_profile or .zshrc, add:

# JAVA,
# Your java 6 version here
export JAVA_HOME=/Library/Java/JavaVirtualMachines/1.6.0_51-b11-457.jdk/Contents/Home

function setjdk() {
    if [ $# -ne 0 ]; then
        removeFromPath '/System/Library/Frameworks/JavaVM.framework/Home/bin'
        if [ -n "${JAVA_HOME+x}" ]; then
            removeFromPath $JAVA_HOME
        fi
        export JAVA_HOME=`/usr/libexec/java_home -v $@`
        export PATH=$JAVA_HOME/bin:$PATH
    fi
    echo JAVA_HOME set to $JAVA_HOME
    java -version
}
function removeFromPath() {
    export PATH=$(echo $PATH | sed -E -e "s;:$1;;" -e "s;$1:?;;")
}

Those functions allow you to quickly switch for java 6 to java 7 and vice-versa:

$> setjdk 1.6  # java 6
$> setjdk 1.7  # java 7
@rezmont
rezmont commented Dec 5, 2013

Thanks kikohs. I am one step closer. 👍
Now I pass the NullExpectionError (that used to occur just as I was opening the file.) But I still can not see my network. It takes my Mac to the rainbow cursor mode, like it is trying to render the graph but it can not. it is a simple graph with 7 nodes and 49 edges and weights and stuff, so nothing super fancy. As I said it works on the ubuntu box.

@kikohs kikohs closed this Dec 5, 2013
@kikohs kikohs reopened this Dec 5, 2013
@kikohs
kikohs commented Dec 5, 2013

Oups, sorry.
Does the example in gephi works ? (Les misérables)

@rezmont
rezmont commented Dec 5, 2013

I just copied a sample graph from here: (https://gephi.org/users/supported-graph-formats/csv-format/) into a csv file and the same thing happened. the it tells me how many nodes and edges are there and the type of the graph which directed/undirected and lablahblah, but then when click ok, it goes to same unresponsive mode. :(

@kikohs
kikohs commented Dec 5, 2013

I already encountered this issue ....
Go in Data laboratory, then import CSV data from here, it should work.

@rezmont
rezmont commented Dec 5, 2013

I'm glad you mentioned it, now that I clicked on Data Lib, again it froze. it is not just that. I tried with a sample gexf file (since the file that I have is of that type) and it broke. I also tried generate a random graph with the program and it broke again. I really think there is something wrong with the rendering engine, or whatever it is called in gephi.

@jatinganhotra

@aarellano Thanks a ton!!! After downloading Java 1.6 and updating the Gephi conf file, it worked like a charm :)

@samoscart

On a Mac (OSX Lion 10.7.5) make sure you delete :

/Users/YourUserName/Library/Application Support/gephi

as stated above. The "Library" directory is/(can be) a hidden directory (/Users/YourUserName/Library/). The hidden directory does not display in "Finder" but is listed in "Terminal".

("/Users/YourUserName/Library/Application Support/"i is not the same as "/Macintosh HD/Library/Application Support")

@neil-rubens
Contributor

@aarellano Thanks a lot; your instructions have worked for me as well.

@salamanders

Is anyone currently working with OS X Mavericks and any recent build (0.8.2 or snapshot)? I get an error of refusing to start with Java 6 from the snapshot, and the 0.8.2 freezes up with the windows displaying garbled.

@rezmont
rezmont commented May 6, 2014

I gave up on it. I am just using it inside my virtual machine.
If anybody has a solution, I would seriously appreciate it.

~RM

On Tue, May 6, 2014 at 9:39 AM, salamanders notifications@github.comwrote:

Is anyone currently working with OS X Mavericks and any recent build
(0.8.2 or snapshot)? I get an error of refusing to start with Java 6 from
the snapshot, and the 0.8.2 freezes up with the windows displaying garbled.


Reply to this email directly or view it on GitHubhttps://github.com/gephi/gephi/issues/748#issuecomment-42326627
.

@joernhees

This took me a while as well :-/
As this is a show-stopper for every normal Mac user here the steps to get it running on Mac OS X 10.9:

  1. download and install this: http://support.apple.com/kb/DL1572
  2. delete your gephi settings dir: rm -r ~/Library/Application\ Support/gephi
  3. find your java home with /usr/libexec/java_home -v 1.6, it should print something like /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
  4. if there is a message about being unable to find any JVMs matching version 1.6 something is wrong, fix it
  5. edit /Applications/Gephi.app/Contents/Resources/gephi/etc/gephi.conf to set your jdkhome e.g. like this:
    echo "jdkhome=\"$(/usr/libexec/java_home -v 1.6)\"" >> /Applications/Gephi.app/Contents/Resources/gephi/etc/gephi.conf
  6. start gephi and open the Les Miserables sample, if you see the graph good.
  7. check gephi's about for the line saying Java: 1.6.0_65; Java HotSpot(TM) 64-Bit Server VM 20.65-b04-462

as simple as that ^^

This critical bug was reported over a year ago... Until Java 7 is supported I suggest solving it similar to other apps like yEd by a dialog guiding the user through the installation of Java 6.
In the meantime please just check the Java Version on startup and properly explain the problem and how to solve it instead of that ugly nothing saying "unable to load libjogl_awt" error message.

We all like gephi, but due to this i guess only < 1 % of your mac users are left :(

@hashar
hashar commented May 22, 2014

With Oracle java 7 I get a NPE:

WARNING [org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings]: The property "netbeans.default_userdir_root" was not set!
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:745)

Found in "~/Library/Application Support/gephi/0.8.2/dev/var/log/messages.log"

@dramalho

@joernhees solution works great :) , unfortunately I was using gephi with the neo4j plugin and that requires JAVA >= 1.7 (sic) . A workaround of course is to start Gephi with the newest java, ignore the things you can't do, import the neo4j DB, export it to a different format and start gephi with 1.6.

That works fine :) , but yeah, I suppose it puts people off quite a bit

@rezmont
rezmont commented Sep 26, 2014

Does anybody notice that gephi breaks with every new releaase of netbeans.
Mine on my ubunutu broke again and does not respend to any of my java
alternative.

here is the message:
$ ./gephi -h
Usage: ./../platform/lib/nbexec {options} arguments

General options:
--help show this help
--jdkhome path to Java(TM) 2 SDK, Standard Edition
-J<jvm_option> pass <jvm_option> to JVM

--cp:p prepend to classpath
--cp:a append to classpath
Exception in thread "main" java.lang.IllegalStateException:
java.lang.IllegalAccessException:
Class org.openide.util.WeakListenerImpl$ProxyListener can not access a
member of class org.openide.filesystems.$Proxy0 with modifiers "public"
at org.openide.util.WeakListenerImpl$ProxyListener.<init

(WeakListenerImpl.java:423)
at org.openide.util.WeakListenerImpl.create(WeakListenerImpl.java:164)
at org.openide.util.WeakListeners.create(WeakListeners.java:271)
at org.openide.filesystems.MultiFileObject.(MultiFileObject.java:125)
at org.openide.filesystems.MultiFileObject.(MultiFileObject.java:142)
at org.openide.filesystems.MultiFileSystem.getMultiRoot(MultiFileSystem.java
:267)
at org.openide.filesystems.MultiFileSystem.findResource(MultiFileSystem.java
:355)
at org.openide.filesystems.FileUtil.getConfigFile(FileUtil.java:2276)
at org.openide.filesystems.FileUtil.getConfigRoot(FileUtil.java:2306)
at org.netbeans.core.startup.CLICoreBridge.usage(CLICoreBridge.java:107)
at org.netbeans.CLIHandler.showHelp(CLIHandler.java:162)
at org.netbeans.CLIHandler.checkHelp(CLIHandler.java:216)
at org.netbeans.CLIHandler.initialize(CLIHandler.java:567)
at org.netbeans.CLIHandler.initialize(CLIHandler.java:383)
at org.netbeans.MainImpl.execute(MainImpl.java:190)
at org.netbeans.MainImpl.main(MainImpl.java:85)
at org.netbeans.Main.main(Main.java:78)
Caused by: java.lang.IllegalAccessException: Class
org.openide.util.WeakListenerImpl$ProxyListener
can not access a member of class org.openide.filesystems.$Proxy0 with
modifiers "public"
at sun.reflect.Reflection.ensureMemberAccess(Reflection.java:101)
at java.lang.reflect.AccessibleObject.slowCheckMemberAccess(
AccessibleObject.java:295)
at java.lang.reflect.AccessibleObject.checkAccess(AccessibleObject.java:287)
at java.lang.reflect.Constructor.newInstance(Constructor.java:398)
at org.openide.util.WeakListenerImpl$ProxyListener.<init
(WeakListenerImpl.java:413)
... 16 more


I have trried all of these:

There are 3 choices for the alternative java (providing /usr/bin/java).

Selection Path Priority

Status

  • 0 /usr/lib/jvm/java-8-oracle/jre/bin/java 2003
    auto mode
    1 /opt/java/64/jre1.7.0_55/bin/java 2000
    manual mode
    2 /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java 1071
    manual mode
    3 /usr/lib/jvm/java-8-oracle/jre/bin/java 2003
    manual mode

Regards,
~RM

On Fri, Sep 26, 2014 at 1:34 AM, David Ramalho notifications@github.com
wrote:

@joernhees https://github.com/joernhees solution works great :) ,
unfortunately I was using gephi with the neo4j plugin and that requires
JAVA >= 1.7 (sic) . A workaround of course is to start Gephi with the
newest java, ignore the things you can't do, import the neo4j DB, export it
to a different format and start gephi with 1.6.

That works fine :) , but yeah, I suppose it puts people off quite a bit


Reply to this email directly or view it on GitHub
#748 (comment).

@berniehogan

its likely the same bug, though. That is, a new OS release resets the java
version and you have you find a way to use the old java version. I haven't
upgraded yet, so I can't walk people through.

Take care,
BERNiE

Dr Bernie Hogan
Research Fellow, Oxford Internet Institute
University of Oxford
http://www.oii.ox.ac.uk/people/hogan

On Fri, Sep 26, 2014 at 11:37 AM, Reza Motamedi notifications@github.com
wrote:

Does anybody notice that gephi breaks with every new releaase of netbeans.
Mine on my ubunutu broke again and does not respend to any of my java
alternative.

here is the message:
$ ./gephi -h
Usage: ./../platform/lib/nbexec {options} arguments

General options:
--help show this help
--jdkhome path to Java(TM) 2 SDK, Standard Edition
-J<jvm_option> pass <jvm_option> to JVM

--cp:p prepend to classpath
--cp:a append to classpath
Exception in thread "main" java.lang.IllegalStateException:
java.lang.IllegalAccessException:
Class org.openide.util.WeakListenerImpl$ProxyListener can not access a
member of class org.openide.filesystems.$Proxy0 with modifiers "public"
at org.openide.util.WeakListenerImpl$ProxyListener.<init

(WeakListenerImpl.java:423)
at org.openide.util.WeakListenerImpl.create(WeakListenerImpl.java:164)
at org.openide.util.WeakListeners.create(WeakListeners.java:271)
at
org.openide.filesystems.MultiFileObject.(MultiFileObject.java:125)
at
org.openide.filesystems.MultiFileObject.(MultiFileObject.java:142)
at
org.openide.filesystems.MultiFileSystem.getMultiRoot(MultiFileSystem.java
:267)
at
org.openide.filesystems.MultiFileSystem.findResource(MultiFileSystem.java
:355)
at org.openide.filesystems.FileUtil.getConfigFile(FileUtil.java:2276)
at org.openide.filesystems.FileUtil.getConfigRoot(FileUtil.java:2306)
at org.netbeans.core.startup.CLICoreBridge.usage(CLICoreBridge.java:107)
at org.netbeans.CLIHandler.showHelp(CLIHandler.java:162)
at org.netbeans.CLIHandler.checkHelp(CLIHandler.java:216)
at org.netbeans.CLIHandler.initialize(CLIHandler.java:567)
at org.netbeans.CLIHandler.initialize(CLIHandler.java:383)
at org.netbeans.MainImpl.execute(MainImpl.java:190)
at org.netbeans.MainImpl.main(MainImpl.java:85)
at org.netbeans.Main.main(Main.java:78)
Caused by: java.lang.IllegalAccessException: Class
org.openide.util.WeakListenerImpl$ProxyListener
can not access a member of class org.openide.filesystems.$Proxy0 with
modifiers "public"
at sun.reflect.Reflection.ensureMemberAccess(Reflection.java:101)
at java.lang.reflect.AccessibleObject.slowCheckMemberAccess(
AccessibleObject.java:295)
at
java.lang.reflect.AccessibleObject.checkAccess(AccessibleObject.java:287)
at java.lang.reflect.Constructor.newInstance(Constructor.java:398)
at org.openide.util.WeakListenerImpl$ProxyListener.<init
(WeakListenerImpl.java:413)
... 16 more


I have trried all of these:

There are 3 choices for the alternative java (providing /usr/bin/java).

Selection Path Priority

Status

  • 0 /usr/lib/jvm/java-8-oracle/jre/bin/java 2003
    auto mode
    1 /opt/java/64/jre1.7.0_55/bin/java 2000
    manual mode
    2 /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java 1071
    manual mode
    3 /usr/lib/jvm/java-8-oracle/jre/bin/java 2003
    manual mode

Regards,
~RM

On Fri, Sep 26, 2014 at 1:34 AM, David Ramalho notifications@github.com
wrote:

@joernhees https://github.com/joernhees solution works great :) ,
unfortunately I was using gephi with the neo4j plugin and that requires
JAVA >= 1.7 (sic) . A workaround of course is to start Gephi with the
newest java, ignore the things you can't do, import the neo4j DB, export
it
to a different format and start gephi with 1.6.

That works fine :) , but yeah, I suppose it puts people off quite a bit


Reply to this email directly or view it on GitHub
#748 (comment).


Reply to this email directly or view it on GitHub
#748 (comment).

@ianfiske
ianfiske commented Oct 3, 2014

@dramalho I have the same dilemma. I'm trying to use Gephi + Neo4j on Mac OS 10.9 Mavericks. I can get Gephi to stop crashing by forcing it to use java 1.6, but then can't use the Neo4j plugin.

@dramalho
dramalho commented Oct 3, 2014

yeah, importing with the latest version of JAVA, then exporting the project to a gephi project and restarting in Java 1.6 and re-importing (ufff, catch your breath there) ... works :)

@ssllmit
ssllmit commented Dec 8, 2014

@dramalho @ianfiske, Same problem on Yosemite, 10.10.1. Pointing Gephi at Apple's Java 6 JDK home works, but Gephi projects that require Java 7 do not. I've tested older Java 7 versions and even gone to the trouble of tricking out Java's OS X version checking bug http://musingsofatechnologist.blogspot.com/2014/08/how-to-install-java-on-yosemite.html, but still no joy.

I've concluded that the only option is to use Gephi on a Linux VM.

@alexwang58

Same problem, but solved finally.
After I download and run https://support.apple.com/kb/DL1572?locale=zh_CN
I change the link "CurrentJDK" to "JDK1.8". Because of this setting, even I set jdk1.6 in gephi.conf and innbexec, gephi still can not found "libjogl_awt".

BTW, this post is more clear :http://sumnous.github.io/blog/2014/07/24/gephi-on-mac/
"CurrentJDK" location is "/System/Library/Frameworks/JavaVM.framework/Versions"

This was referenced Aug 26, 2015
@eduramiba eduramiba added this to the 0.9 milestone Aug 26, 2015
@eduramiba eduramiba added the windows label Aug 26, 2015
@bfontaine
Contributor

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

@mbastian
Member

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.

@mbastian mbastian closed this Dec 12, 2015
@mbastian mbastian changed the title from [critical] Gephi is broken MacOS X 10.8.2 with java 7 to Gephi isn't compatible with Java 7 and 8 on all platforms (Windows, Mac OS X, Linux) Dec 12, 2015
@mbastian mbastian added Fix Released and removed Fix Committed labels Dec 22, 2015
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment