0.8.2 on Mac OS X 10.8.2 with Java 1.7

[brianckeegan]

I'm having trouble with launching Gephi 0.8.2 on Mac OS X 10.8.2. On launch, the program will load but then hang with all the text labels disappearing:



I suspect the problem is related to updates to Java, as other users have been having. Following the advice of previous threads, I installed the latest version of Java 6 from Apple. However, 4 March 2013 release removes the Application utility referenced in previous documentation. After install of Apple Java 6, however I cannot find it thus I cannot follow prior advice about how to point Gephi toward it.

For example, trying solutions such as adding a symbolic link don't apply because I can only find the Java 7 installation in the /Library/Java/JavaVirtualMachine/ tree:

Code: Select all

$ cd /Library/Java/JavaVirtualMachines/
$ ls
1.7.0.jdk

And the only version visible to the environment appears to be:

Code: Select all

$ java -version
java version "1.7.0_05"
Java(TM) SE Runtime Environment (build 1.7.0_05-b06)

Based on the previous thread, I believe that I just need someone to tell me the command to set the CurrentJDK symlink from 1.7 (which is all I can see) to 1.6 (which I installed but can't find).

The ouput from Gephi's log file for reference:

Code: Select all

-------------------------------------------------------------------------------
>Log Session: Thursday, March 14, 2013 12:45:13 PM EDT
>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_05; Java HotSpot(TM) 64-Bit Server VM 23.1-b03; Oracle Corporation
  Runtime                 = Java(TM) SE Runtime Environment 1.7.0_05-b06
  Java Home               = /Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/jre
  System Locale; Encoding = en_US (gephi); US-ASCII
  Home Directory          = /Users/brianckeegan
  Current Directory       = /
  User Directory          = /Users/brianckeegan/Library/Application Support/gephi/0.8.2/dev
  Cache Directory         = /Users/brianckeegan/Library/Application Support/gephi/0.8.2/dev/var/cache
  Installation            = /Applications/Gephi.app/Contents/Resources/gephi/gephi
                            /Applications/Gephi.app/Contents/Resources/gephi/platform
                            /Applications/Gephi.app/Contents/Resources/gephi/platform
  Boot & Ext. Classpath   = /Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/jre/lib/resources.jar:/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/jre/lib/rt.jar:/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/jre/lib/sunrsasign.jar:/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/jre/lib/jsse.jar:/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/jre/lib/jce.jar:/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/jre/lib/charsets.jar:/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/jre/lib/jfr.jar:/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/jre/lib/JObjC.jar:/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/jre/classes:/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/jre/lib/ext/dnsns.jar:/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/jre/lib/ext/localedata.jar:/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/jre/lib/ext/sunec.jar:/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/jre/lib/ext/sunjce_provider.jar:/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/jre/lib/ext/sunpkcs11.jar:/Library/Java/JavaVirtualMachines/1.7.0.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   = /Applications/Gephi.app/Contents/Resources/gephi/platform/lib/boot.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/org-openide-modules.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/org-openide-util-lookup.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/org-openide-util.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ar_SA.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_bg.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ca.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_cs.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_de.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_es.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_fr.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_gl_ES.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_in_ID.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_it.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ja.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ko.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_nl_NL.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_pl.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_pt_BR.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_pt_PT.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ro.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ru.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_si.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_sq.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_sv.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_tr.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_zh_CN.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_zh_TW.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ar_SA.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_bg.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ca.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_cs.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_de.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_es.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_fr.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_gl_ES.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_in_ID.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_it.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ja.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ko.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_nl_NL.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_pl.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_pt_BR.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_pt_PT.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ro.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ru.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_si.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_sq.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_sv.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_tr.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_zh_CN.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_zh_TW.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_bg.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ca.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_cs.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_de.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_es.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_fr.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_gl_ES.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_in_ID.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_it.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ja.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ko.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_nl_NL.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_pl.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_pt_BR.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ro.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ru.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_si.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_sv.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_tr.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_zh_CN.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ar_SA.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_bg.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ca.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_cs.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_de.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_es.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_fr.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_gl_ES.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_in_ID.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_it.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ja.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ko.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_nl_NL.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_pl.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_pt_BR.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_pt_PT.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ro.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ru.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_si.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_sq.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_sv.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_tr.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_zh_CN.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_zh_TW.jar:/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/lib/dt.jar:/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/lib/tools.jar
  Startup Classpath       = /Applications/Gephi.app/Contents/Resources/gephi/platform/core/core.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/org-openide-filesystems.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_ar_SA.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_bg.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_ca.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_cs.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_de.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_es.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_fr.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_gl_ES.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_in_ID.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_it.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_ja.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_ko.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_nl_NL.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_pl.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_pt_BR.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_pt_PT.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_ro.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_ru.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_si.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_sq.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_sv.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_tr.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_zh_CN.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/core_zh_TW.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ar_SA.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_bg.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ca.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_cs.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_de.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_es.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_fr.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_gl_ES.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_in_ID.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_it.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ja.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ko.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_nl_NL.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_pl.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_pt_BR.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_pt_PT.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ro.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ru.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_si.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_sq.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_sv.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_tr.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_zh_CN.jar:/Applications/Gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_zh_TW.jar:/Applications/Gephi.app/Contents/MacOS/../Resources/gephi/bin/../gephi/core/locale/core_gephi.jar
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WARNING [org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings]: The property "netbeans.default_userdir_root" was not set!
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@645e5018[org.gephi.visualization] with possible defining loaders null and declared parents [ModuleCL@3e4cb5a3[org.gephi.dynamic.api], ModuleCL@343526f3[org.gephi.ui.library.wrapper], ModuleCL@9a3da81[org.gephi.gleem], ModuleCL@90affbc[org.gephi.tools.api], ModuleCL@243634f2[org.openide.awt], ModuleCL@46160dbd[org.openide.dialogs], ModuleCL@7ce5b708[org.gephi.graph.api], ModuleCL@311b9447[org.gephi.utils.collection], ModuleCL@4d53ae47[org.gephi.data.attributes.api], ModuleCL@7f611b48[org.netbeans.modules.settings], ...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:1262)
	at sun.lwawt.LWComponentPeer.handleEvent(LWComponentPeer.java:1150)
	at java.awt.Component.dispatchEventImpl(Component.java:4937)
	at java.awt.Component.dispatchEvent(Component.java:4687)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:703)
	at java.awt.EventQueue.access$000(EventQueue.java:102)
	at java.awt.EventQueue$3.run(EventQueue.java:662)
	at java.awt.EventQueue$3.run(EventQueue.java:660)
	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:676)
	at java.awt.EventQueue$4.run(EventQueue.java:674)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:673)
	at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:158)
[catch] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:244)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:163)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:151)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:147)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:139)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:97)
Diagnostic information
Input arguments:
	-Djdk.home=/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home
	-Dnetbeans.system_http_proxy=DIRECT
	-Dnetbeans.system_http_non_proxy_hosts=
	-Dnetbeans.dirs=/Applications/Gephi.app/Contents/MacOS/../Resources/gephi/bin/../gephi:/Applications/Gephi.app/Contents/MacOS/../Resources/gephi/bin/../platform:
	-Dnetbeans.home=/Applications/Gephi.app/Contents/Resources/gephi/platform
	-Dcom.apple.mrj.application.apple.menu.about.name=gephi
	-Xms64m
	-Xmx512m
	-Xverify:none
	-Dsun.java2d.noddraw=true
	-Dsun.awt.noerasebackground=true
	-Dnetbeans.indexing.noFileRefresh=true
	-Dplugin.manager.check.interval=EVERY_DAY
	-XX:+HeapDumpOnOutOfMemoryError
	-XX:HeapDumpPath=/Users/brianckeegan/Library/Application Support/gephi/0.8.2/dev/var/log/heapdump.hprof
Compiler: HotSpot 64-Bit Tiered Compilers
Heap memory usage: initial 64.0MB maximum 455.1MB
Non heap memory usage: initial 23.2MB maximum 130.0MB
Garbage collector: PS Scavenge (Collections=7 Total time spent=0s)
Garbage collector: PS MarkSweep (Collections=0 Total time spent=0s)
Classes: loaded=5943 total loaded=5943 unloaded 0
INFO [org.netbeans.core.ui.warmup.DiagnosticTask]: Total memory 6,442,450,944
INFO [null]: Total physical memory 6,442,450,944
WARNING [org.netbeans.modules.autoupdate.updateproviders.AutoupdateCatalogFactory]: Services/AutoupdateType/org_gephi_branding_update_center.instance: url_key attribute deprecated in favor of url
WARNING [org.netbeans.modules.autoupdate.updateproviders.AutoupdateCatalogFactory]: Services/AutoupdateType/org_gephi_branding_update_center_1.instance: url_key attribute deprecated in favor of url
WARNING [org.netbeans.modules.autoupdate.updateprovider.AutoupdateCatalogParser]: http://gephi.org/updates/official/0.8.2/catalog.xml:15:10: The content of element type "module" must match "(description?,module_notification?,external_package*,(manifest|l10n))".
[...]

exception in QueueFlusher:
javax.media.opengl.GLException: Attempt to make the same context current twice on thread Thread[Java2D Queue Flusher,10,system]
	at com.sun.opengl.impl.GLContextLock.lock(GLContextLock.java:83)
	at com.sun.opengl.impl.GLContextImpl.makeCurrent(GLContextImpl.java:131)
	at com.sun.opengl.impl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:182)
	at javax.media.opengl.GLCanvas$DisplayOnEventDispatchThreadAction.run(GLCanvas.java:452)
	at sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run(OGLRenderQueue.java:234)
exception in QueueFlusher:
javax.media.opengl.GLException: Attempt to make the same context current twice on thread Thread[Java2D Queue Flusher,10,system]
	at com.sun.opengl.impl.GLContextLock.lock(GLContextLock.java:83)
	at com.sun.opengl.impl.GLContextImpl.makeCurrent(GLContextImpl.java:131)
	at com.sun.opengl.impl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:182)
	at javax.media.opengl.GLCanvas$DisplayOnEventDispatchThreadAction.run(GLCanvas.java:452)
	at sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run(OGLRenderQueue.java:234)
exception in QueueFlusher:
javax.media.opengl.GLException: Attempt to make the same context current twice on thread Thread[Java2D Queue Flusher,10,system]
	at com.sun.opengl.impl.GLContextLock.lock(GLContextLock.java:83)
	at com.sun.opengl.impl.GLContextImpl.makeCurrent(GLContextImpl.java:131)
	at com.sun.opengl.impl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:182)
	at javax.media.opengl.GLCanvas$DisplayOnEventDispatchThreadAction.run(GLCanvas.java:452)
	at sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run(OGLRenderQueue.java:234)
exception in QueueFlusher:
javax.media.opengl.GLException: Attempt to make the same context current twice on thread Thread[Java2D Queue Flusher,10,system]
	at com.sun.opengl.impl.GLContextLock.lock(GLContextLock.java:83)
	at com.sun.opengl.impl.GLContextImpl.makeCurrent(GLContextImpl.java:131)
	at com.sun.opengl.impl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:182)
	at javax.media.opengl.GLCanvas$DisplayOnEventDispatchThreadAction.run(GLCanvas.java:452)
	at sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run(OGLRenderQueue.java:234)
exception in QueueFlusher:
javax.media.opengl.GLException: Attempt to make the same context current twice on thread Thread[Java2D Queue Flusher,10,system]
	at com.sun.opengl.impl.GLContextLock.lock(GLContextLock.java:83)
	at com.sun.opengl.impl.GLContextImpl.makeCurrent(GLContextImpl.java:131)
	at com.sun.opengl.impl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:182)
	at javax.media.opengl.GLCanvas$DisplayOnEventDispatchThreadAction.run(GLCanvas.java:452)
	at sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run(OGLRenderQueue.java:234)

[brianckeegan]

A few other diagnostics:

Code: Select all

$ ls -l /System/Library/Frameworks/JavaVM.framework/Versions/
total 64
lrwxr-xr-x  1 root  wheel   10 Mar 14 14:41 1.4 -> CurrentJDK
lrwxr-xr-x  1 root  wheel   10 Mar 14 14:41 1.4.2 -> CurrentJDK
lrwxr-xr-x  1 root  wheel   10 Mar 14 14:41 1.5 -> CurrentJDK
lrwxr-xr-x  1 root  wheel   10 Mar 14 14:41 1.5.0 -> CurrentJDK
lrwxr-xr-x  1 root  wheel   10 Mar 14 14:41 1.6 -> CurrentJDK
lrwxr-xr-x  1 root  wheel   10 Mar 14 14:41 1.6.0 -> CurrentJDK
drwxr-xr-x  8 root  wheel  272 Mar 14 14:41 A
lrwxr-xr-x  1 root  wheel    1 Mar 14 14:41 Current -> A
lrwxr-xr-x  1 root  wheel   59 Mar 14 14:41 CurrentJDK -> /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents

Code: Select all

$ sudo ln -s /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/bin/java
ln: ./java: File exists
$ java -version
java version "1.7.0_05"
Java(TM) SE Runtime Environment (build 1.7.0_05-b06)
Java HotSpot(TM) 64-Bit Server VM (build 23.1-b03, mixed mode)

[brianckeegan]

Uninstalling 1.7, I can no longer replicate the crash in Gephi. This leads me to believe that having 1.7 breaks Gephi (as others have noted on GitHub) and this fact should be noted more prominently until it can be fixed.

Code: Select all

$ sudo rm -rf /Library/Java/JavaVirtualMachines/1.7.0.jdk
$ java -version
java version "1.6.0_43"
Java(TM) SE Runtime Environment (build 1.6.0_43-b01-447-11M4203)
Java HotSpot(TM) 64-Bit Server VM (build 20.14-b01-447, mixed mode)

[eduramiba]

Hi,
Thanks for the report.
We are already aware of this problem of Java 7 and MacOS https://github.com/gephi/gephi/issues/748

I recommend to use Java 6 in Mac until this is solved.

Eduardo

[louiejre]

I am currently running Java 1.6, but Gephi does not start. It cannot pass Open Main Window screen. The menu bar loads, but there is no item under each menu. Can someone please help me?

Code: Select all

java version "1.6.0_43"
Java(TM) SE Runtime Environment (build 1.6.0_43-b01-447-11M4203)
Java HotSpot(TM) 64-Bit Server VM (build 20.14-b01-447, mixed mode)

[louiejre]

I am still having problem starting the application. It does not start. No panel is loaded at all. It only loads a big box with grey background. At the bottom of the screen says Open Main Window. The message disappears after two seconds, but the grey box stays.

I followed instructions from another thread, added a symbolic link to JDK, and added jdkhome to gephi.conf, but no difference was observed.

Code: Select all

sudo ln -s /Library/Java/JavaVirtualMachines/1.6.0_43-b01-447.jdk/Contents /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK

jdkhome="/Library/Java/JavaVirtualMachines/1.6.0_43-b01-447.jdk/Contents/Home/"

Another interesting thing I found today is the application starts successfully from inside the .dmg file, but it fails from the .app file in the Application folder. According to the installation instructions, the application should be run from the Application folder. I hope someone can provide some ideas to fix my problem. Thanks.

[elraidor]

Same problem - only runs from the .dmg file. Although mine starts, it won't load any files, not even a csv. Did you make any progress on this?