Can't get 0.8 beta to run on Mac OS X 10.7.3

[tomdzk]

Hi,

I'm trying to get Gephi 0.8 beta (downloaded today) running on my Mac (Lion, 10.7.3) and have no success with it:

* 1.6.0_22-b04-307.jdk fails without any error or other message
* 1.6.0_26-b03-383.jdk (my default jdk) fails with "Unable to load libjogl_awt.jnilib"
* OpenJDK 1.7.0-u4-b13 fails with "Init failed : Unsupported os / arch ( Mac OS X / amd64 ). Please check you're using a 32-bit JVM.

Any ideas ?

cheers,
Tom

[mbastian]

That might be related to this issue. Can you give me the list of files you have in the /Library/Java/Extensions/ folder? Thanks.

Gephi is working on Lion normally, I've tested it myself.

[tomdzk]

I only have PostgreSQL in there (for whatever reason):

$ ls /Library/Java/Extensions
postgresql-8.3-603.jdbc3.jar

and a

find /Library/Java/ -iname "*ogl*"

doesn't show anything either.

[mbastian]

Ok so that's not the issue. Can you please look if you have a messages.log file in

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/Users/username/Library/Application/Support/gephi

and if yes paste it here

[tomdzk]

Running this:

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/Applications/gephi.app/Contents/MacOS/gephi --jdkhome /Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Home

using the gephi stable 0.8-beta build gives me

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-------------------------------------------------------------------------------
>Log Session: Sunday, March 4, 2012 12:03:46 PM PST
>System Info: 
  Product Version         = Gephi 0.8 beta
  Operating System        = Mac OS X version 10.7.3 running on x86_64
  Java; VM; Vendor        = 1.6.0_26; Java HotSpot(TM) 64-Bit Server VM 20.1-b02-383; Apple Inc.
  Runtime                 = Java(TM) SE Runtime Environment 1.6.0_26-b03-383-11D50b
  Java Home               = /Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Home
  System Locale; Encoding = en_US (gephi); MacRoman
  Home Directory          = /Users/tomdz
  Current Directory       = /Users/tomdz
  User Directory          = /Users/tomdz/Library/Application Support/gephi/dev
  Installation            = /Applications/gephi.app/Contents/Resources/gephi/gephi
                            /Applications/gephi.app/Contents/Resources/gephi/platform
  Boot & Ext. Classpath   = /Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Classes/jsfd.jar:/Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Classes/classes.jar:/System/Library/Frameworks/JavaVM.framework/Frameworks/JavaRuntimeSupport.framework/Resources/Java/JavaRuntimeSupport.jar:/Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Classes/ui.jar:/Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Classes/laf.jar:/Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Classes/sunrsasign.jar:/Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Classes/jsse.jar:/Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Classes/jce.jar:/Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Classes/charsets.jar:/Library/Java/Extensions/postgresql-8.3-603.jdbc3.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:/Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Home/lib/ext/apple_provider.jar:/Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Home/lib/ext/dnsns.jar:/Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Home/lib/ext/localedata.jar:/Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Home/lib/ext/sunjce_provider.jar:/Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Home/lib/ext/sunpkcs11.jar
  Application Classpath   = /Applications/gephi.app/Contents/Resources/gephi/platform/lib/boot.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/org-openide-modules.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/org-openide-util-lookup.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/org-openide-util.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ar_SA.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_pt_PT.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_sq.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_zh_TW.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ar_SA.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_pt_PT.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_sq.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_zh_TW.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ar_SA.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_pt_PT.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_sq.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_zh_TW.jar:/Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Home/lib/dt.jar
  Startup Classpath       = /Applications/gephi.app/Contents/Resources/gephi/platform/core/core.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/org-openide-filesystems.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ar_SA.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_pt_PT.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_sq.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_zh_TW.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ar_SA.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_pt_PT.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_sq.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_zh_TW.jar:/Applications/gephi.app/Contents/MacOS/../Resources/gephi/bin/../gephi/core/locale/core_gephi.jar
-------------------------------------------------------------------------------
WARNING [org.netbeans.core.modules]: the modules [org.gephi.desktop.preview, org.gephi.ui.exporter.plugin, org.gephi.ui.filters.plugin, org.gephi.ui.statistics.plugin] use org.jdesktop.layout which is deprecated: Use javax.swing.GroupLayout instead. (In form editor: select Form ... in Inspector; change Layout Generation Style to Standard Java 6 code.)
Loading native libraries

Running gephi with the older JDK

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/Applications/gephi.app/Contents/MacOS/gephi --jdkhome /Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Home/

gives me this instead:

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-------------------------------------------------------------------------------
>Log Session: Sunday, March 4, 2012 12:06:20 PM PST
>System Info: 
  Product Version         = Gephi 0.8 beta
  Operating System        = Mac OS X version 10.7.3 running on x86_64
  Java; VM; Vendor        = 1.6.0_22; Java HotSpot(TM) 64-Bit Server VM 17.1-b03-307; Apple Inc.
  Runtime                 = Java(TM) SE Runtime Environment 1.6.0_22-b04-307-11D50b
  Java Home               = /Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Home
  System Locale; Encoding = en_US (gephi); MacRoman
  Home Directory          = /Users/tomdz
  Current Directory       = /Users/tomdz
  User Directory          = /Users/tomdz/Library/Application Support/gephi/dev
  Installation            = /Applications/gephi.app/Contents/Resources/gephi/gephi
                            /Applications/gephi.app/Contents/Resources/gephi/platform
  Boot & Ext. Classpath   = /Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Classes/jsfd.jar:/Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Classes/classes.jar:/System/Library/Frameworks/JavaVM.framework/Frameworks/JavaRuntimeSupport.framework/Resources/Java/JavaRuntimeSupport.jar:/Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Classes/ui.jar:/Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Classes/laf.jar:/Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Classes/sunrsasign.jar:/Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Classes/jsse.jar:/Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Classes/jce.jar:/Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Classes/charsets.jar:/Library/Java/Extensions/postgresql-8.3-603.jdbc3.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:/Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Home/lib/ext/apple_provider.jar:/Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Home/lib/ext/dnsns.jar:/Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Home/lib/ext/localedata.jar:/Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Home/lib/ext/sunjce_provider.jar:/Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Home/lib/ext/sunpkcs11.jar
  Application Classpath   = /Applications/gephi.app/Contents/Resources/gephi/platform/lib/boot.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/org-openide-modules.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/org-openide-util-lookup.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/org-openide-util.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ar_SA.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_pt_PT.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_sq.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/boot_zh_TW.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ar_SA.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_pt_PT.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_sq.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-modules_zh_TW.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util-lookup_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ar_SA.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_pt_PT.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_sq.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/lib/locale/org-openide-util_zh_TW.jar:/Library/Java/JavaVirtualMachines/1.6.0_22-b04-307.jdk/Contents/Home/lib/dt.jar
  Startup Classpath       = /Applications/gephi.app/Contents/Resources/gephi/platform/core/core.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/org-openide-filesystems.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ar_SA.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_pt_PT.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_sq.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/core_zh_TW.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ar_SA.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ca.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_cs.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_de.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_es.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_fr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_gl_ES.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_in_ID.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_it.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ja.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ko.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_nl_NL.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_pl.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_pt_BR.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_pt_PT.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ro.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_ru.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_sq.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_sv.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_tr.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_zh_CN.jar:/Applications/gephi.app/Contents/Resources/gephi/platform/core/locale/org-openide-filesystems_zh_TW.jar:/Applications/gephi.app/Contents/MacOS/../Resources/gephi/bin/../gephi/core/locale/core_gephi.jar
-------------------------------------------------------------------------------
WARNING [org.netbeans.core.modules]: the modules [org.gephi.desktop.preview, org.gephi.ui.exporter.plugin, org.gephi.ui.filters.plugin, org.gephi.ui.statistics.plugin] use org.jdesktop.layout which is deprecated: Use javax.swing.GroupLayout instead. (In form editor: select Form ... in Inspector; change Layout Generation Style to Standard Java 6 code.)
java.lang.NoClassDefFoundError: apple/laf/CoreUIControl
	at com.apple.laf.AquaLookAndFeel$1.run(AquaLookAndFeel.java:124)
	at java.security.AccessController.doPrivileged(Native Method)
	at com.apple.laf.AquaLookAndFeel.initialize(AquaLookAndFeel.java:121)
	at javax.swing.UIManager.setLookAndFeel(UIManager.java:519)
	at javax.swing.UIManager.setLookAndFeel(UIManager.java:564)
	at javax.swing.UIManager.initializeDefaultLAF(UIManager.java:1329)
	at javax.swing.UIManager.initialize(UIManager.java:1422)
	at javax.swing.UIManager.maybeInitialize(UIManager.java:1410)
	at javax.swing.UIManager.getLookAndFeel(UIManager.java:473)
	at org.netbeans.swing.plaf.Startup.getLookAndFeel(Startup.java:166)
	at org.netbeans.swing.plaf.Startup.initialize(Startup.java:115)
	at org.netbeans.swing.plaf.Startup.<init>(Startup.java:108)
	at org.netbeans.swing.plaf.Startup.run(Startup.java:486)
	at org.netbeans.core.CoreBridgeImpl.initializePlaf(CoreBridgeImpl.java:124)
	at org.netbeans.core.startup.Main.initUICustomizations(Main.java:144)
	at org.netbeans.core.startup.NbInstaller.load(NbInstaller.java:361)
	at org.netbeans.ModuleManager.enable(ModuleManager.java:1025)
	at org.netbeans.core.startup.ModuleList.installNew(ModuleList.java:318)
	at org.netbeans.core.startup.ModuleList.trigger(ModuleList.java:254)
	at org.netbeans.core.startup.ModuleSystem.restore(ModuleSystem.java:294)
	at org.netbeans.core.startup.Main.getModuleSystem(Main.java:172)
	at org.netbeans.core.startup.Main.start(Main.java:308)
	at org.netbeans.core.startup.TopThreadGroup.run(TopThreadGroup.java:123)
	at java.lang.Thread.run(Thread.java:680)

[tomdzk]

Fwiw, setting LD_LIBRARY_PATH or DYLD_LIBRARY_PATH, e.g.

Code: Select all

export LD_LIBRARY_PATH="/Applications/gephi.app/Contents/Resources/gephi/gephi/modules/lib/macosx-universal/"
export DYLD_LIBRARY_PATH="/Applications/gephi.app/Contents/Resources/gephi/gephi/modules/lib/macosx-universal/"

or passing java.library.path on the command line, e.g.

Code: Select all

/Applications/gephi.app/Contents/MacOS/gephi --jdkhome /Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Home/ -J-Djava.library.path=/Applications/gephi.app/Contents/Resources/gephi/gephi/modules/lib/macosx-universal/

don't seem to make any difference.

[tomdzk]

A quick test program showed that the libjogl_awt library is linked against /System/Library/Frameworks/JavaVM.framework/Libraries/libjawt.dylib, however that path is not created anymore with more recent apple jdk's.
Creating it manually via

Code: Select all

sudo ln -s /Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK

fixed the problem for me and Gephi now starts.
Maybe the gephi start script could in the 'darwin' case check for the existence of '/System/Library/Frameworks/JavaVM.framework/Libraries/' and warn/error out when it does not exist ?

[mbastian]

Thanks for this detailed investigation. Sounds like this is a serious issue as Gephi won't start without that library. I couldn't really find any official documentation mentionning these virtual links being removed.

We have our own library loader in the JOGL Wrapper module and we could add something like below for Mac OS X:

Code: Select all

//Make sure jawt is loaded on mac os x
File defaultJdk = new File("/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK");
if (!defaultJdk.exists()) {
   String javaHome = System.getProperty("java.home");
   javaHome = javaHome.substring(0, javaHome.lastIndexOf("Home"));
   defaultJdk = new File(javaHome);
}
File libraryPath = new File(defaultJdk, "Libraries");
if (libraryPath.exists()) {
   loadLibrary(new File(libraryPath, "libjawt.dylib"));
} else {
   System.out.println("Can't locate the default Libraries folder");
}

That should find the current JDK 'Libraries' folder in any case and directly load the library. That would happen before we load the 'jogl_awt' library so it should be fine. What do you think?

[tomdzk]

That should work, though it would be nice if the error message would be a bit more detailed (e.g. 'please make sure that '.../CurrentJDK' is a symbolic link that points to your current java installation), and is shown in the popup error window. Maybe a link to a FAQ entry in the error window ?
Also, MacOS has a useful tool, /usr/libexec/java_home, that returns the current java home (without needing to set JAVA_HOME), e.g.

Code: Select all

$ /usr/libexec/java_home 
/Library/Java/JavaVirtualMachines/1.6.0_26-b03-383.jdk/Contents/Home

in my case. That might be useful to find the java to use for gephi.

[albertocottica]

Hello Bastian and all, I have 10.7.4 and can't get Gephi started either. I tried Tom's sudo command, but my machine informs me that the file exists.

Also, I have no directory called gephi in

Code: Select all

/Users/username/Library/Application Support

I am really hoping you guys have some ideas here...