What "open" in file menu?

[-jn-]

Downloaded Gephi 0.7 alpha 3 to MacBookPro running Java6 on OS X 10.5.8; attempted to follow the "quick start" tutorial, and hit the wall on slide 2. Instructions were "In the menubar, go to File Menu and Open... " but after launching Gephi the File menu only has "Export", "Save", "Save As...", "Save All", "Page Setup...", and "Print...", with all but "Page Setup..." grayed out. http://tweetphoto.com/16844331

For what it's worth, the "Graph" window is gibbering to itself with what looks like a rapid succession of numbers in the general vicinity of "30.0" constantly being written to the upper left corner of the screen.

Any suggestions on how I get the program to a sane state tot run the tutorial?

[mbastian]

Hi,

This bug is currently the most critical one, it has been already reported here an on the bug tracker.

I need to get the execution log to fix it, could you find it and copy it here?

On Mac it shouls be in /youruser/Library/Application support/gephidesktop/dev/var/log/messages.log

Thanks

[-jn-]

Here is one from a fresh run this morning:

Code: Select all

-------------------------------------------------------------------------------
>Log Session: Saturday, April 3, 2010 9:13:33 AM CDT
>System Info: 
  Product Version         = Gephi 0.7 alpha3 200912041610
  Operating System        = Mac OS X version 10.5.8 running on x86_64
  Java; VM; Vendor        = 1.6.0_17; Java HotSpot(TM) 64-Bit Server VM 14.3-b01-101; Apple Inc.
  Runtime                 = Java(TM) SE Runtime Environment 1.6.0_17-b04-248-9M3125
  Java Home               = /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home
  System Locale; Encoding = en_US (gephidesktop); MacRoman
  Home Directory          = /Users/joel
  Current Directory       = /
  User Directory          = /Users/joel/Library/Application Support/gephidesktop/dev
  Installation            = /Applications/gephi-0.7-alpha3.app/Contents/Resources/gephidesktop/gephidesktop
                            /Applications/gephi-0.7-alpha3.app/Contents/Resources/gephidesktop/platform11
  Boot & Ext. Classpath   = /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jsfd.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/classes.jar:/System/Library/Frameworks/JavaVM.framework/Frameworks/JavaRuntimeSupport.framework/Resources/Java/JavaRuntimeSupport.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/ui.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/laf.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/sunrsasign.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jsse.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jce.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/charsets.jar:/System/Library/Java/Extensions/AppleScriptEngine.jar:/System/Library/Java/Extensions/CoreAudio.jar:/System/Library/Java/Extensions/dns_sd.jar:/System/Library/Java/Extensions/j3daudio.jar:/System/Library/Java/Extensions/j3dcore.jar:/System/Library/Java/Extensions/j3dutils.jar:/System/Library/Java/Extensions/jai_codec.jar:/System/Library/Java/Extensions/jai_core.jar:/System/Library/Java/Extensions/mlibwrapper_jai.jar:/System/Library/Java/Extensions/MRJToolkit.jar:/System/Library/Java/Extensions/QTJava.zip:/System/Library/Java/Extensions/vecmath.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/ext/apple_provider.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/ext/dnsns.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/ext/localedata.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/ext/sunjce_provider.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/ext/sunpkcs11.jar
  Application Classpath   = /Applications/gephi-0.7-alpha3.app/Contents/Resources/gephidesktop/platform11/lib/boot.jar:/Applications/gephi-0.7-alpha3.app/Contents/Resources/gephidesktop/platform11/lib/org-openide-modules.jar:/Applications/gephi-0.7-alpha3.app/Contents/Resources/gephidesktop/platform11/lib/org-openide-util.jar:/Applications/gephi-0.7-alpha3.app/Contents/Resources/gephidesktop/platform11/lib/locale/org-openide-util_ja.jar:/Applications/gephi-0.7-alpha3.app/Contents/Resources/gephidesktop/platform11/lib/locale/org-openide-util_pt_BR.jar:/Applications/gephi-0.7-alpha3.app/Contents/Resources/gephidesktop/platform11/lib/locale/org-openide-util_zh_CN.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6/Home/lib/dt.jar
  Startup Classpath       = /Applications/gephi-0.7-alpha3.app/Contents/Resources/gephidesktop/platform11/core/core.jar:/Applications/gephi-0.7-alpha3.app/Contents/Resources/gephidesktop/platform11/core/org-openide-filesystems.jar:/Applications/gephi-0.7-alpha3.app/Contents/MacOS/../Resources/gephidesktop/bin/../gephidesktop/core/locale/core_gephidesktop.jar
-------------------------------------------------------------------------------
WARNING [org.netbeans.core.startup.NbEvents]: The extension /Applications/gephi-0.7-alpha3.app/Contents/Resources/gephidesktop/gephidesktop/modules/ext/beansbinding-1.2.1.jar may be multiply loaded by modules: [/Applications/gephi-0.7-alpha3.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-ui-utils.jar, /Applications/gephi-0.7-alpha3.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-desktop-tools.jar]; see: http://www.netbeans.org/download/dev/javadoc/org-openide-modules/org/openide/modules/doc-files/classpath.html#class-path
WARNING [org.openide.filesystems.Ordering]: Not all children in Services/MIMEResolver/ marked with the position attribute: [GephiResolver.xml], but some are: [instance-mime-resolver.xml]
WARNING [org.openide.filesystems.Ordering]: Not all children in Services/MIMEResolver/ marked with the position attribute: [GephiResolver.xml], but some are: [instance-mime-resolver.xml]
Loading native libraries
INFO [org.netbeans.core.startup.NbEvents]: Turning on modules:
	org.openide.util [7.31.2.1 1 201001291424]
	org.openide.modules [7.13.1 200912041610]
	org.jdesktop.swingx [1.6 100331]
	org.gephi.ui.utils [0.7 100331]
	org.openide.awt [7.19.1.1 200912041610]
	org.netbeans.libs.junit4 [1.7.1 200912041610]
	org.netbeans.api.progress/1 [1.16.1.1 1 200912041610]
	org.gephi.utils.longtask [0.7.0.1 100331]
	org.openide.filesystems [7.32.1.1.1 1 200912041610]
	org.gephi.desktop.mrufiles.api [0.7 100331]
	org.jdesktop.layout/1 [1.10.1.103 103 200912041610]
	org.openide.dialogs [7.13.1 200912041610]
	org.openide.nodes [7.12.1.1 200912041610]
	org.openide.windows [6.30.1 200912041610]
	org.netbeans.modules.editor.mimelookup/1 [1.14.1 200912041610]
	org.openide.text [6.27.1 200912041610]
	org.netbeans.swing.outline [1.7.1 200912041610]
	org.openide.explorer [6.22.2.1 1 201001291424]
	org.openide.actions [6.12.1.1 200912041610]
	org.netbeans.modules.queries/1 [1.17.1 200912041610]
	org.openide.loaders [7.10.1 200912041610]
	org.gephi.project.api [0.7.0.3 100331]
	org.gephi.graph.api [0.7.0.2 100331]
	org.gephi.clustering.api [0.7 100331]
	org.netbeans.spi.quicksearch [1.4.1 200912041610]
	org.netbeans.bootstrap/1 [2.22.1 200912041610]
	org.netbeans.core.startup/1 [1.19.1.1 200912041610]
	org.netbeans.modules.autoupdate.services [1.16.2 201003241801]
	org.openide.io [1.20.1 200912041610]
	org.netbeans.swing.plaf [1.12.1 200912041610]
	org.netbeans.core/2 [3.14.1.1 200912041610]
	org.netbeans.modules.options.api/1 [1.16.2 201001291424]
	org.netbeans.modules.options.keymap [1.8.1 200912041610]
	org.netbeans.libs.jna/1 [1.5.1 200912041610]
	org.netbeans.modules.settings/1 [1.22.1.1 200912041610]
	org.netbeans.swing.tabcontrol [1.19.1 200912041610]
	org.netbeans.core.windows/2 [2.17.1.1 200912041610]
	org.netbeans.core.nativeaccess/1 [1.5.1 200912041610]
	org.netbeans.core.io.ui/1 [1.4.1.1 1 200912041610]
	org.gephi.data.attributes.api [0.7 100331]
	org.gephi.ui.components [0.7 100331]
	org.gephi.statistics.api [0.7 100331]
	org.jfree [1.0 100331]
	org.gephi.statistics.plugin [0.7.0.1 100331]
	org.gephi.ui.statistics.plugin [0.7.0.2 100331]
	org.gephi.algorithms [0.7 100331]
	org.netbeans.modules.progress.ui [1.6.1.1 200912041610]
	org.gephi.lib.batik [1.7 100331]
	org.gephi.ui.workspace [0.7 100331]
	org.netbeans.modules.editor.mimelookup.impl/1 [1.7.1 200912041610]
	org.gephi.clustering.plugin [0.7 100331]
	org.gephi.ui.project [0.7 100331]
	org.gephi.layout.api [0.7 100331]
	org.gephi.desktop.layout [0.7.0.1 100331]
	org.gephi.preview.api [0.7.0.2 100331]
	org.gephi.tools.api [0.7 100331]
	org.gephi.lib.gleem [1.0 100331]
	org.gephi.lib.jogl [1.1.0.1 100331]
	org.gephi.utils.collection [0.7 100331]
	org.gephi.lib.validation [0.4 100331]
	org.gephi.visualization [0.7.0.7 100331]
	org.gephi.desktop.hierarchy [0.7.0.1 100331]
	org.gephi.tools.plugin [0.7 100331]
	org.gephi.io.exporter.api [0.7 100331]
	org.gephi.io.exporter.plugin [0.7.0.1 100331]
	org.gephi.ui.exporter.plugin [0.7.0.1 100331]
	org.gephi.ui.propertyeditor [0.7 100331]
	org.gephi.data.attributes [0.7 100331]
	org.gephi.lib.processing [1.0.9 100331]
	org.netbeans.modules.print [7.3.1 200912041610]
	org.gephi.desktop.context [0.7.0.1 100331]
	org.gephi.partition.api [0.7.0.2 100331]
	org.gephi.desktop.partition [0.7.0.1 100331]
	org.netbeans.modules.favorites/1 [1.18.1 200912041610]
	org.netbeans.swing.dirchooser [1.0 100331]
	org.gephi.ranking.api [0.7 100331]
	org.gephi.ui.ranking.plugin [0.7 100331]
	org.gephi.graph.dhns [0.7.0.4 100331]
	org.gephi.layout.plugin [0.7 100331]
	org.gephi.filters.api [0.7 100331]
	org.netbeans.modules.applemenu/1 [1.14.1 200912041610]
	org.gephi.desktop.tools [0.7.0.1 100331]
	org.gephi.ui.components.SplineEditor [0.7 100331]
	org.gephi.desktop.filters [0.7.0.4 100331]
	org.gephi.desktop.io.export [0.7.0.3 100331]
	org.gephi.desktop.preview [0.7.0.2 100331]
	org.gephi.desktop.clustering [0.7 100331]
	org.netbeans.modules.masterfs/2 [2.20.1 200912041610]
	org.gephi.ui.datatable [0.7 100331]
	org.gephi.desktop.statistics [0.7 100331]
	org.gephi.preview [0.7.0.2 100331]
	org.gephi.partition.plugin [0.7 100331]
	org.netbeans.modules.autoupdate.ui [1.14.1 200912041610]
	org.gephi.desktop.ranking [0.7.0.1 100331]
	org.gephi.io.exporter.preview [0.7 100331]
	org.netbeans.core.ui/1 [1.19.2.1 201001291424]
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: NVIDIA GeForce 8600M GT OpenGL Engine
GL_VERSION: 2.0 NVIDIA-1.5.48
Diagnostic information
Input arguments:
	-Djdk.home=/System/Library/Frameworks/JavaVM.framework/Versions/1.6/Home
	-Dnetbeans.system_http_proxy=DIRECT
	-Dnetbeans.system_http_non_proxy_hosts=
	-Dnetbeans.dirs=/Applications/gephi-0.7-alpha3.app/Contents/MacOS/../Resources/gephidesktop/bin/../gephidesktop:
	-Dnetbeans.home=/Applications/gephi-0.7-alpha3.app/Contents/Resources/gephidesktop/platform11
	-Dcom.apple.mrj.application.apple.menu.about.name=gephidesktop
	-Xms64m
	-Xmx256m
	-XX:+HeapDumpOnOutOfMemoryError
	-XX:HeapDumpPath=/Users/joel/Library/Application
	Support/gephidesktop/dev/var/log/heapdump.hprof
Compiler: HotSpot 64-Bit Server Compiler
Heap memory usage: initial 64.0MB maximum 252.0MB
Non heap memory usage: initial 23.2MB maximum 132.0MB
Garbage collector: ParNew (Collections=6 Total time spent=0s)
Garbage collector: ConcurrentMarkSweep (Collections=2 Total time spent=0s)
Classes: loaded=5264 total loaded=5264 unloaded 0
INFO [org.netbeans.core.ui.warmup.DiagnosticTask]: Total memory 2,147,483,648
INFO [null]: Total physical memory 2,147,483,648
WARNING [org.openide.filesystems.Ordering]: Not all children in Menu/Window/ marked with the position attribute: [ClusteringAction.shadow, ContextAction.shadow, DataTableAction.shadow, FiltersAction.shadow, GraphAction.shadow, HierarchyAction.shadow, LayoutAction.shadow, PartitionAction.shadow, PreviewAction.shadow, PreviewSettingsAction.shadow, RankingAction.shadow, StatisticsAction.shadow], but some are: [ViewFavoritesTabAction.shadow, org-netbeans-core-windows-actions-GlobalPropertiesAction.shadow, Output, SwitchToRecentDocumentAction.shadow, ProgressListAction.shadow, Separator3.instance, CloseWindowAction.shadow, MaximizeWindowAction.shadow, org-netbeans-core-windows-actions-UndockAction.shadow, Separator4.instance, CloneDocumentAction.shadow, CloseAllDocumentsAction.shadow, CloseAllButThisAction.shadow, DocumentsAction.shadow, Separator5.instance, org-netbeans-core-windows-actions-ResetWindowsAction.shadow]

[mbastian]

Thanks a lot! No issue seems obvious in the log file at the first lecture :/ I'll see what I can find and I keep you updated here.

[Dan Bumbarger]

I am having the same issue.

Code: Select all

-------------------------------------------------------------------------------
>Log Session: Sunday, May 9, 2010 12:35:47 PM CEST
>System Info: 
  Product Version         = Gephi 0.7 alpha4 200912041610
  Operating System        = Mac OS X version 10.5.8 running on x86_64
  Java; VM; Vendor        = 1.6.0_17; Java HotSpot(TM) 64-Bit Server VM 14.3-b01-101; Apple Inc.
  Runtime                 = Java(TM) SE Runtime Environment 1.6.0_17-b04-248-9M3125
  Java Home               = /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home
  System Locale; Encoding = en_US (gephidesktop); MacRoman
  Home Directory          = /Users/dan
  Current Directory       = /
  User Directory          = /Users/dan/Library/Application Support/gephidesktop/dev
  Installation            = /Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop
                            /Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/platform11
  Boot & Ext. Classpath   = /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jsfd.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/classes.jar:/System/Library/Frameworks/JavaVM.framework/Frameworks/JavaRuntimeSupport.framework/Resources/Java/JavaRuntimeSupport.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/ui.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/laf.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/sunrsasign.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jsse.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jce.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/charsets.jar:/System/Library/Java/Extensions/AppleScriptEngine.jar:/System/Library/Java/Extensions/CoreAudio.jar:/System/Library/Java/Extensions/dns_sd.jar:/System/Library/Java/Extensions/j3daudio.jar:/System/Library/Java/Extensions/j3dcore.jar:/System/Library/Java/Extensions/j3dutils.jar:/System/Library/Java/Extensions/jai_codec.jar:/System/Library/Java/Extensions/jai_core.jar:/System/Library/Java/Extensions/mlibwrapper_jai.jar:/System/Library/Java/Extensions/MRJToolkit.jar:/System/Library/Java/Extensions/QTJava.zip:/System/Library/Java/Extensions/vecmath.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/ext/apple_provider.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/ext/dnsns.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/ext/localedata.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/ext/sunjce_provider.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/ext/sunpkcs11.jar
  Application Classpath   = /Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/platform11/lib/boot.jar:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/platform11/lib/org-openide-modules.jar:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/platform11/lib/org-openide-util.jar:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/platform11/lib/locale/org-openide-util_ja.jar:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/platform11/lib/locale/org-openide-util_pt_BR.jar:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/platform11/lib/locale/org-openide-util_zh_CN.jar:/System/Library/Frameworks/JavaVM.framework/Versions/1.6/Home/lib/dt.jar
  Startup Classpath       = /Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/platform11/core/core.jar:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/platform11/core/org-openide-filesystems.jar:/Applications/gephi-0.7-alpha4.app/Contents/MacOS/../Resources/gephidesktop/bin/../gephidesktop/core/locale/core_gephidesktop.jar
-------------------------------------------------------------------------------
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-io-exporter-api.jar!/org/gephi/io/exporter/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-preview-api.jar!/org/gephi/preview/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-graph-api.jar!/org/gephi/graph/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-ui-project.jar!/org/gephi/ui/project/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-data-attributes-api.jar!/org/gephi/data/attributes/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-io-exporter-plugin.jar!/org/gephi/io/exporter/plugin/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-ui-components-SplineEditor.jar!/org/gephi/ui/components/SplineEditor/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-tools-api.jar!/org/gephi/tools/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-ui-components.jar!/org/gephi/ui/components/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-layout-api.jar!/org/gephi/layout/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-layout-plugin.jar!/org/gephi/layout/plugin/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-filters-api.jar!/org/gephi/filters/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-ranking-api.jar!/org/gephi/ranking/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-ui-ranking-plugin.jar!/org/gephi/ui/ranking/plugin/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-statistics-api.jar!/org/gephi/statistics/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-statistics-plugin.jar!/org/gephi/statistics/plugin/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-ui-statistics-plugin.jar!/org/gephi/ui/statistics/plugin/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-ui-workspace.jar!/org/gephi/ui/workspace/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-partition-api.jar!/org/gephi/partition/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-clustering-api.jar!/org/gephi/clustering/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/gephidesktop/modules/org-gephi-algorithms.jar!/org/gephi/algorithms/layer.xml
Loading native libraries
INFO [org.netbeans.core.startup.NbEvents]: Turning on modules:
	org.openide.util [7.31.2.1 1 201001291424]
	org.openide.modules [7.13.1 200912041610]
	org.jfree [1.0 100430]
	org.openide.awt [7.19.1.1 200912041610]
	org.jdesktop.layout/1 [1.10.1.103 103 200912041610]
	org.netbeans.api.progress/1 [1.16.1.1 1 200912041610]
	org.openide.dialogs [7.13.1 200912041610]
	org.openide.nodes [7.12.1.1 200912041610]
	org.openide.windows [6.30.1 200912041610]
	org.netbeans.modules.progress.ui [1.6.1.1 200912041610]
	org.gephi.lib.itext [5.0.1 100430]
	org.netbeans.libs.junit4 [1.7.1 200912041610]
	org.gephi.utils.longtask [0.7.0.2 100430]
	org.openide.filesystems [7.32.1.1.1 1 200912041610]
	org.gephi.project.api [0.7.0.5 100430]
	org.gephi.lib.batik [1.7 100430]
	org.gephi.io.exporter.api [0.7 100430]
	org.gephi.preview.api [0.7.0.3 100430]
	org.gephi.io.exporter.preview [0.7.0.2 100430]
	org.jdesktop.swingx [1.6 100430]
	org.gephi.lib.validation [0.4 100430]
	org.gephi.ui.exporter.preview [0.7 100430]
	org.gephi.ui.utils [0.7.0.1 100430]
	org.gephi.graph.api [0.7.0.2 100430]
	org.netbeans.swing.outline [1.7.1 200912041610]
	org.openide.explorer [6.22.2.1 1 201001291424]
	org.netbeans.modules.editor.mimelookup/1 [1.14.1 200912041610]
	org.openide.text [6.27.1 200912041610]
	org.openide.actions [6.12.1.1 200912041610]
	org.netbeans.modules.queries/1 [1.17.1 200912041610]
	org.openide.loaders [7.10.1 200912041610]
	org.netbeans.bootstrap/1 [2.22.1 200912041610]
	org.netbeans.core.startup/1 [1.19.1.1 200912041610]
	org.openide.io [1.20.1 200912041610]
	org.netbeans.swing.plaf [1.12.1 200912041610]
	org.netbeans.core/2 [3.14.1.1 200912041610]
	org.netbeans.modules.settings/1 [1.22.1.1 200912041610]
	org.gephi.desktop.context [0.7.0.1 100430]
	org.gephi.ui.project [0.7.0.1 100430]
	org.gephi.desktop.mrufiles.api [0.7 100430]
	org.gephi.lib.beansbinding [1.2.1 100430]
	org.gephi.data.attributes.api [0.7 100430]
	org.gephi.io.exporter.plugin [0.7.0.3 100430]
	org.gephi.ui.exporter.plugin [0.7.0.4 100430]
	org.gephi.ui.components.SplineEditor [0.7 100430]
	org.gephi.tools.api [0.7 100430]
	org.gephi.visualization.api [0.7 100430]
	org.netbeans.spi.quicksearch [1.4.1 200912041610]
	org.netbeans.modules.options.api/1 [1.16.2 201001291424]
	org.gephi.lib.gleem [1.0 100430]
	org.gephi.lib.jogl [1.1.0.1 100430]
	org.gephi.utils.collection [0.7 100430]
	org.gephi.ui.components [0.7 100430]
	org.gephi.visualization [0.7.0.10 100430]
	org.gephi.ui.propertyeditor [0.7 100430]
	org.gephi.layout.api [0.7.0.1 100430]
	org.gephi.layout.plugin [0.7.0.2 100430]
	org.gephi.filters.api [0.7.0.2 100430]
	org.gephi.filters [0.7.0.1 100430]
	org.gephi.ranking.api [0.7 100430]
	org.gephi.ui.ranking.plugin [0.7 100430]
	org.gephi.statistics.api [0.7 100430]
	org.gephi.statistics.plugin [0.7.0.2 100430]
	org.gephi.ui.statistics.plugin [0.7.0.2 100430]
	org.gephi.ui.workspace [0.7 100430]
	org.netbeans.modules.print [7.3.1 200912041610]
	org.gephi.desktop.io.export [0.7.0.4 100430]
	org.gephi.lib.processing [1.0.9 100430]
	org.gephi.desktop.preview [0.7.0.4 100430]
	org.gephi.partition.api [0.7.0.3 100430]
	org.netbeans.swing.tabcontrol [1.19.1 200912041610]
	org.gephi.clustering.api [0.7 100430]
	org.netbeans.modules.autoupdate.services [1.16.2 201003241801]
	org.gephi.desktop.layout [0.7.0.1 100430]
	org.gephi.desktop.tools [0.7.0.4 100430]
	org.gephi.algorithms [0.7.0.1 100430]
	org.netbeans.core.windows/2 [2.17.1.1 200912041610]
	org.netbeans.modules.applemenu/1 [1.14.1 200912041610]
	org.netbeans.libs.jna/1 [1.5.1 200912041610]
	org.gephi.desktop.statistics [0.7.0.3 100430]
	org.netbeans.modules.editor.mimelookup.impl/1 [1.7.1 200912041610]
	org.gephi.partition.plugin [0.7 100430]
	org.netbeans.core.ui/1 [1.19.2.1 201001291424]
	org.gephi.clustering.plugin [0.7 100430]
	org.netbeans.core.nativeaccess/1 [1.5.1 200912041610]
	org.netbeans.core.io.ui/1 [1.4.1.1 1 200912041610]
	org.gephi.desktop.clustering [0.7 100430]
	org.netbeans.modules.autoupdate.ui [1.14.1 200912041610]
	org.netbeans.modules.masterfs/2 [2.20.1 200912041610]
	org.gephi.desktop.filters [0.7.0.9 100430]
	org.gephi.preview [0.7.0.3 100430]
	org.gephi.ui.datatable [0.7 100430]
	org.gephi.desktop.ranking [0.7.0.1 100430]
	org.netbeans.modules.favorites/1 [1.18.1 200912041610]
	org.gephi.desktop.hierarchy [0.7.0.3 100430]
	org.netbeans.swing.dirchooser [1.0 100430]
	org.gephi.graph.dhns [0.7.0.5 100430]
	org.gephi.desktop.progress [0.7 100430]
	org.gephi.data.attributes [0.7 100430]
	org.netbeans.modules.options.keymap [1.8.1 200912041610]
	org.gephi.tools.plugin [0.7.0.2 100430]
	org.gephi.desktop.partition [0.7.0.1 100430]
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: NVIDIA GeForce 9400M OpenGL Engine
GL_VERSION: 2.0 NVIDIA-1.5.48
Diagnostic information
Input arguments:
	-Djdk.home=/System/Library/Frameworks/JavaVM.framework/Versions/1.6/Home
	-Dnetbeans.system_http_proxy=DIRECT
	-Dnetbeans.system_http_non_proxy_hosts=
	-Dnetbeans.dirs=/Applications/gephi-0.7-alpha4.app/Contents/MacOS/../Resources/gephidesktop/bin/../gephidesktop:
	-Dnetbeans.home=/Applications/gephi-0.7-alpha4.app/Contents/Resources/gephidesktop/platform11
	-Dcom.apple.mrj.application.apple.menu.about.name=gephidesktop
	-Xms64m
	-Xmx256m
	-XX:+HeapDumpOnOutOfMemoryError
	-XX:HeapDumpPath=/Users/dan/Library/Application
	Support/gephidesktop/dev/var/log/heapdump.hprof
Compiler: HotSpot 64-Bit Server Compiler
Heap memory usage: initial 64.0MB maximum 252.0MB
Non heap memory usage: initial 23.2MB maximum 132.0MB
Garbage collector: ParNew (Collections=7 Total time spent=0s)
Garbage collector: ConcurrentMarkSweep (Collections=2 Total time spent=0s)
Classes: loaded=5265 total loaded=5265 unloaded 0
INFO [org.netbeans.core.ui.warmup.DiagnosticTask]: Total memory 4,294,967,296
INFO [null]: Total physical memory 4,294,967,296
WARNING [org.openide.filesystems.Ordering]: Found same position 1200 for both Menu/Window/Output and Menu/Window/RankingAction.shadow
WARNING [org.openide.filesystems.Ordering]: Found same position 800 for both Menu/Window/LayoutAction.shadow and Menu/Window/org-netbeans-core-windows-actions-GlobalPropertiesAction.shadow

[mbastian]

Hi, thanks for reporting the problem. I'm a bit confused how this could happen, as I though we fixed the problem in the alpha4 versions. It seems another problem is there I'll dig it.

[tbenton]

I'm running into precisely this same problem, running an identical setup to the original poster. Should it be possible to run an older version of Gephi until this is fixed? I have downloaded several but am not finding any application files, unfortunately.

[mbastian]

I made an update today, among other things trying to fix this problem.

Are you able to update your current Gephi version and then restart it?

[tbenton]

I'm afraid it doesn't. Screen shot of the open menu, for what this is worth:

[jdudley]

I just did a fresh install of Gephi alpha 4 on Mac OS X 10.5.8 running Java 6 SE and I am having the same problem. The "Open" command is nowhere to be found in the menu, and I can't even open the example files listed on the Welcome screen.