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Home Page: http://gephi.org
License: GNU General Public License v3.0
Gephi - The Open Graph Viz Platform
Home Page: http://gephi.org
License: GNU General Public License v3.0
Statistics reports are not updated.
Way to reproduce :
The report is the same.
Imported from Launchpad using lp2gh.
Way to reproduce:
Stack trace:
java.lang.IllegalArgumentException: Level must be between 0 and the height of the tree, currently height=9
at org.gephi.graph.dhns.graph.HierarchicalGraphImpl.getLevelSize(HierarchicalGraphImpl.java:166)
at org.gephi.desktop.hierarchy.HierarchyControlPanel.initLevelsLinks(HierarchyControlPanel.java:176)
at org.gephi.desktop.hierarchy.HierarchyControlPanel.setup(HierarchyControlPanel.java:140)
at org.gephi.desktop.hierarchy.HierarchyPropertyBarAddon$HierarchyAddonButton.createPopup(HierarchyPropertyBarAddon.java:88)
at org.gephi.desktop.hierarchy.HierarchyPropertyBarAddon$HierarchyAddonButton.access$000(HierarchyPropertyBarAddon.java:65)
at org.gephi.desktop.hierarchy.HierarchyPropertyBarAddon$HierarchyAddonButton$1.actionPerformed(HierarchyPropertyBarAddon.java:80)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
Imported from Launchpad using lp2gh.
After importing a graph (codeminer.gexf), if you select all the nodes and try to delete them, the following Exception is thrown:
java.lang.NullPointerException
at org.gephi.graph.dhns.utils.avl.AbstractEdgeTree.remove(AbstractEdgeTree.java:239)
at org.gephi.graph.dhns.core.GraphStructure.removeFromDictionnary(GraphStructure.java:165)
at org.gephi.graph.dhns.core.StructureModifier$Business.deleteNode(StructureModifier.java:384)
at org.gephi.graph.dhns.core.StructureModifier$Business.access$400(StructureModifier.java:277)
at org.gephi.graph.dhns.core.StructureModifier.deleteNode(StructureModifier.java:103)
at org.gephi.graph.dhns.graph.HierarchicalGraphImpl.removeNode(HierarchicalGraphImpl.java:202)
at org.gephi.visualization.bridge.DHNSEventBridge.delete(DHNSEventBridge.java:380)
at org.gephi.visualization.apiimpl.GraphContextMenu$7.actionPerformed(GraphContextMenu.java:116)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at javax.swing.AbstractButton.doClick(AbstractButton.java:357)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1223)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1264)
at java.awt.Component.processMouseEvent(Component.java:6263)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6028)
at java.awt.Container.processEvent(Container.java:2041)
at java.awt.Component.dispatchEventImpl(Component.java:4630)
at java.awt.Container.dispatchEventImpl(Container.java:2099)
at java.awt.Component.dispatchEvent(Component.java:4460)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
at java.awt.Container.dispatchEventImpl(Container.java:2085)
at java.awt.Component.dispatchEvent(Component.java:4460)
[catch] at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:137)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Imported from Launchpad using lp2gh.
Any attempt at exporting immediately throws a NullPointerException. This is triggered either by selecting any option from the "File > Export" menu, or pressing the "SVG" button in the Preview Settings window.
SVG Export:
java.lang.NullPointerException
at org.gephi.desktop.io.export.api.VectorialFileExporterUI.action(VectorialFileExporterUI.java:178)
at org.gephi.desktop.io.export.Export$2.actionPerformed(Export.java:71)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
at com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:95)
at java.awt.MenuItem.processActionEvent(MenuItem.java:627)
at java.awt.MenuItem.processEvent(MenuItem.java:586)
at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:317)
at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:305)
[catch] at java.awt.EventQueue.dispatchEvent(EventQueue.java:638)
at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:125)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Graph Export:
java.lang.NullPointerException
at org.gephi.desktop.io.export.api.GraphFileExporterUI.action(GraphFileExporterUI.java:183)
...rest exactly the same...
Imported from Launchpad using lp2gh.
Graphic library error, related to JOGL.
Stack trace:
java.lang.UnsatisfiedLinkError: com.sun.opengl.impl.JAWTFactory.JAWT_GetAWT0(Ljava/nio/ByteBuffer;)Z
at com.sun.opengl.impl.JAWTFactory.JAWT_GetAWT0(Native Method)
at com.sun.opengl.impl.JAWTFactory.JAWT_GetAWT(JAWTFactory.java:38)
at com.sun.opengl.impl.JAWT$1.run(JAWT.java:99)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.opengl.impl.JAWT.getJAWT(JAWT.java:95)
at com.sun.opengl.impl.macosx.MacOSXOnscreenGLDrawable.lockSurface(MacOSXOnscreenGLDrawable.java:144)
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.maybeDoSingleThreadedWorkaround(GLCanvas.java:412)
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:276)
Found on:
Could be because another bad version of JOGL library is already loaded by another program or from default system path. Looking for solutions...
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Preview component doesn't display meta-edges.
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Way to reproduce:
Average degree and Diameter output 0.
Average Path Length outputs NaN.
etc.
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When exporting a dynamic GEXF with Gephi, the "start" and "end" attributes are missing.
By example, here is a node from the imported GEXF :
and the resulting GEXF, when exporting from Gephi :
In consequence, and until the bug is fixed, be aware to not export a dynamic GEXF with the same name that the original, or you will lost the dynamic data.
Imported from Launchpad using lp2gh.
Way to reproduce:
Stack Trace:
java.lang.NullPointerException
at org.gephi.graph.dhns.edge.AbstractEdge.getUndirected(AbstractEdge.java:92)
at org.gephi.graph.dhns.edge.iterators.EdgeIterator.hasNext(EdgeIterator.java:59)
at org.gephi.graph.dhns.graph.iterators.EdgeIteratorImpl.hasNext(EdgeIteratorImpl.java:44)
at org.gephi.visualization.bridge.DHNSDataBridge.updateEdges(DHNSDataBridge.java:187)
at org.gephi.visualization.bridge.DHNSDataBridge.updateWorld(DHNSDataBridge.java:126)
at org.gephi.visualization.opengl.compatibility.CompatibilityEngine.updateWorld(CompatibilityEngine.java:181)
at org.gephi.visualization.opengl.compatibility.CompatibilityScheduler.updateWorld(CompatibilityScheduler.java:270)
Imported from Launchpad using lp2gh.
When I enable to show nodes' labels in the preview, I can not export in pdf. If I disable the labels, everything works smoothly. The export process go to 100% down and right on the window, but it never disappears. Also the .pdf file that it creates is of 0bytes size.
Way to reproduce:
Tested on Gephi 0.8alpha with latest updates on 28 August 2011.
Imported from Launchpad using lp2gh.
Like the summary says, Gephi can't be built with JDK 7.
The problem is that PDF Exporter depends on the sun.font.FontManager class, which is an "internal proprietary API", according to the build log:
Compiling 3 source files to /home/luiz/projects/bzr/gephi/PreviewExport/build/classes
warning: [options] bootstrap class path not set in conjunction with -source 1.5
/home/luiz/projects/bzr/gephi/PreviewExport/src/org/gephi/io/exporter/preview/PDFExporter.java:68: warning: FontManager is internal proprietary API and may be removed in a future release
import sun.font.FontManager;
Note: org.gephi.io.exporter.preview.ExporterBuilderPDF to be registered as a org.gephi.io.exporter.spi.VectorFileExporterBuilder
/home/luiz/projects/bzr/gephi/PreviewExport/src/org/gephi/io/exporter/preview/PDFExporter.java:68: warning: FontManager is internal proprietary API and may be removed in a future release
import sun.font.FontManager;
/home/luiz/projects/bzr/gephi/PreviewExport/src/org/gephi/io/exporter/preview/PDFExporter.java:68: warning: FontManager is internal proprietary API and may be removed in a future release
import sun.font.FontManager;
/home/luiz/projects/bzr/gephi/PreviewExport/src/org/gephi/io/exporter/preview/PDFExporter.java:467: warning: FontManager is internal proprietary API and may be removed in a future release
String fontName = FontManager.getFileNameForFontName(font.getFontName());
/home/luiz/projects/bzr/gephi/PreviewExport/src/org/gephi/io/exporter/preview/PDFExporter.java:467: error: cannot find symbol
String fontName = FontManager.getFileNameForFontName(font.getFontName());
symbol: method getFileNameForFontName(String)
location: interface FontManager
/home/luiz/projects/bzr/gephi/PreviewExport/src/org/gephi/io/exporter/preview/PDFExporter.java:469: warning: FontManager is internal proprietary API and may be removed in a future release
String fontFilePath = FontManager.getFontPath(false);
/home/luiz/projects/bzr/gephi/PreviewExport/src/org/gephi/io/exporter/preview/PDFExporter.java:469: error: cannot find symbol
String fontFilePath = FontManager.getFontPath(false);
symbol: method getFontPath(boolean)
location: interface FontManager
2 errors
6 warnings
/usr/share/netbeans/harness/common.xml:206: Compile failed; see the compiler error output for details.
BUILD FAILED (total time: 3 seconds)
If I comment the lines 467 to 472 from PDFExporter.java, everything builds just fine, so we just need to find an alternative to calling FontManager's getFileNameForFontName and getFontPath methods.
Imported from Launchpad using lp2gh.
With directed graphs, the Preview mode display wrongly mutual edges weight
See http://forum.gephi.org/viewtopic.php?f=4&t=421&start=0
Dataset:
Gexf.net First test of manually encoded dataImported from Launchpad using lp2gh.
Way to reproduce:
You'll see that the edge (A,C) is not directed but mutual, however it is shown as directed in the Data Lab.
If the edge between A and B is directed, there is no error.
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File > Open Project > Cancel
--> open the file explorer window instead of doing nothing
File > New Project > Cancel
--> reset the project instead of doing nothing
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Have a 20k nodes, 500k edges graph, spatialized with open ord, 4 workspaces with on the first the complete graph and on the 3 followings 3 different subgraph extracted from the main one. Trying to save the file in a gephi format, processing bar stay stucked, memory load is about 7GO (on 8 on my computer) and processor around 50%.
Windows7, 64bits system.
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Meta-edges are not displayed. Works when some normal edge is in the graph.
Way to reproduce:
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The filter does not work with hierarchies.
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The GEXF parser is abnormally using too much memory. This limits its ability to deal with large graphs.
This bug also affects GraphML
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Way to reproduce:
Stack trace:
ClassCastException: org.gephi.filters.OperatorQueryImpl cannot be cast to org.gephi.filters.FilterQueryImpl
java.lang.ClassCastException: org.gephi.filters.OperatorQueryImpl cannot be cast to org.gephi.filters.FilterQueryImpl
at org.gephi.filters.FilterModelImpl.updateParameters(FilterModelImpl.java:167)
at org.gephi.filters.FilterThread.run(FilterThread.java:67)
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Graph API throws NPE because source or target is null
Stack trace:
java.lang.NullPointerException
at org.gephi.graph.dhns.core.GraphFactoryImpl.newEdge(GraphFactoryImpl.java:128)
at org.gephi.graph.dhns.core.GraphFactoryImpl.newEdge(GraphFactoryImpl.java:123)
at org.gephi.graph.dhns.core.GraphFactoryImpl.newEdge(GraphFactoryImpl.java:47)
at org.gephi.datalab.impl.GraphElementsControllerImpl.buildEdge(GraphElementsControllerImpl.java:431)
at org.gephi.datalab.impl.GraphElementsControllerImpl.createEdge(GraphElementsControllerImpl.java:89)
at org.gephi.datalab.impl.AttributeColumnsControllerImpl.importCSVToEdgesTable(AttributeColumnsControllerImpl.java:597)
at org.gephi.datalab.plugin.manipulators.general.ui.ImportCSVUIWizardAction.performAction(ImportCSVUIWizardAction.java:85)
at org.gephi.datalab.plugin.manipulators.general.ImportCSV.execute(ImportCSV.java:40)
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There seems to be an issue with one of the last revisions regarding the weight of edges.
After you import a graph (gml, gexf...) and validate the import report you get the following exception:
java.lang.NullPointerException
at org.gephi.graph.dhns.edge.EdgeDataImpl.getWeight(EdgeDataImpl.java:207)
at org.gephi.graph.dhns.edge.AbstractEdge.getWeight(AbstractEdge.java:71)
at org.gephi.visualization.bridge.DHNSDataBridge.updateEdges(DHNSDataBridge.java:191)
at org.gephi.visualization.bridge.DHNSDataBridge.updateWorld(DHNSDataBridge.java:126)
at org.gephi.visualization.opengl.compatibility.CompatibilityEngine.updateWorld(CompatibilityEngine.java:181)
at org.gephi.visualization.opengl.compatibility.CompatibilityScheduler.updateWorld(CompatibilityScheduler.java:285)
[catch] at org.gephi.visualization.scheduler.SimpleFPSAnimator.run(SimpleFPSAnimator.java:58)
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To reproduce the bug:
With Force Atlas:
First, save some presets for this layout, call it "saved_presets_1"
Second, modify some parameters of the layout and save the presets with the same name as before (saved_presets_1)
=> bug: two occurrences of "saved_presets_1" appear now in the saved presets list.
To correct the situation, one must close and re-open GEPHI: just one (the more recent I suppose) instance remains.
=> not a bug, but related wish list: add a cross next to the name of the presets to be able to delete them (with a window asking for confirmation of deletion!).
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Stack trace:
java.lang.NullPointerException
at org.gephi.graph.dhns.core.Dhns.getIdGen(Dhns.java:123)
at org.gephi.graph.dhns.core.EdgeProcessor.<init>(EdgeProcessor.java:52)
at org.gephi.graph.dhns.core.StructureModifier.<init>(StructureModifier.java:57)
at org.gephi.graph.dhns.core.GraphViewImpl.<init>(GraphViewImpl.java:36)
at org.gephi.graph.dhns.core.GraphStructure.<init>(GraphStructure.java:70)
at org.gephi.graph.dhns.core.Dhns.<init>(Dhns.java:85)
at org.gephi.graph.dhns.DhnsPersistenceProvider.readXML(DhnsPersistenceProvider.java:48)
at org.gephi.project.io.GephiReader.readWorkspaceChildren(GephiReader.java:145)
at org.gephi.project.io.GephiReader.readWorkspace(GephiReader.java:131)
at org.gephi.project.io.GephiReader.readProject(GephiReader.java:104)
at org.gephi.project.io.GephiReader.readAll(GephiReader.java:81)
at org.gephi.project.io.LoadTask.run(LoadTask.java:81)
at org.gephi.desktop.project.ProjectControllerUIImpl$5.run(ProjectControllerUIImpl.java:281)
at org.gephi.utils.longtask.api.LongTaskExecutor$RunningLongTask.run(LongTaskExecutor.java:228)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
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Démarrage de Gephi
Nouveau projet
Import d'un gdf
Je lance Label Ajust et au bout de quelque second fenêtre d'erreur sans message, je peux pas agir dessus car gephi semble continuer de tourner.
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Way to reproduce:
Imported from Launchpad using lp2gh.
Way to reproduce:
Stack trace:
Java.lang.IllegalArgumentException: Node must be in the graph
at org.gephi.graph.dhns.graph.AbstractGraphImpl.checkNode(AbstractGraphImpl.java:127)
at org.gephi.graph.dhns.graph.HierarchicalGraphImpl.getParent(HierarchicalGraphImpl.java:230)
at org.gephi.partition.impl.PartitionControllerImpl.isGroupable(PartitionControllerImpl.java:254)
at org.gephi.desktop.partition.PartitionChooser.refreshGrouped(PartitionChooser.java:332)
at org.gephi.desktop.partition.PartitionChooser.refreshModel(PartitionChooser.java:409)
at org.gephi.desktop.partition.PartitionChooser.setup(PartitionChooser.java:419)
at org.gephi.desktop.partition.PartitionTopComponent.refreshModel(PartitionTopComponent.java:84)
at org.gephi.desktop.partition.PartitionTopComponent.access$000(PartitionTopComponent.java:36)
at org.gephi.desktop.partition.PartitionTopComponent$1.select(PartitionTopComponent.java:66)
at org.gephi.project.impl.ProjectControllerImpl.fireWorkspaceEvent(ProjectControllerImpl.java:287)
at org.gephi.project.impl.ProjectControllerImpl.openWorkspace(ProjectControllerImpl.java:234)
at org.gephi.ui.workspace.WorkspaceUISelectorPanel$2.actionPerformed(WorkspaceUISelectorPanel.java:72)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
at java.awt.Component.processMouseEvent(Component.java:6263)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6028)
at java.awt.Container.processEvent(Container.java:2041)
at java.awt.Component.dispatchEventImpl(Component.java:4630)
at java.awt.Container.dispatchEventImpl(Container.java:2099)
at java.awt.Component.dispatchEvent(Component.java:4460)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
at java.awt.Container.dispatchEventImpl(Container.java:2085)
at java.awt.Window.dispatchEventImpl(Window.java:2478)
at java.awt.Component.dispatchEvent(Component.java:4460)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:125)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Imported from Launchpad using lp2gh.
Gephi running on Windows 7 sometimes throws an Exception when users open file dialogs (Open project, Open, Save As).
Stack:
java.lang.NullPointerException
at javax.swing.ImageIcon.<init>(ImageIcon.java:190)
at javax.swing.ImageIcon.<init>(ImageIcon.java:176)
at sun.swing.WindowsPlacesBar.<init>(WindowsPlacesBar.java:82)
at com.sun.java.swing.plaf.windows.WindowsFileChooserUI.updateUseShellFolder(WindowsFileChooserUI.java:505)
at com.sun.java.swing.plaf.windows.WindowsFileChooserUI.installComponents(WindowsFileChooserUI.java:196)
at javax.swing.plaf.basic.BasicFileChooserUI.installUI(BasicFileChooserUI.java:136)
at com.sun.java.swing.plaf.windows.WindowsFileChooserUI.installUI(WindowsFileChooserUI.java:129)
at javax.swing.JComponent.setUI(JComponent.java:673)
at javax.swing.JFileChooser.updateUI(JFileChooser.java:1763)
at javax.swing.JFileChooser.setup(JFileChooser.java:360)
at javax.swing.JFileChooser.<init>(JFileChooser.java:342)
at javax.swing.JFileChooser.<init>(JFileChooser.java:301)
at org.gephi.branding.desktop.actions.OpenFile.actionPerformed(OpenFile.java:65)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at javax.swing.AbstractButton.doClick(AbstractButton.java:357)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1225)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1266)
at java.awt.Component.processMouseEvent(Component.java:6263)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6028)
at java.awt.Container.processEvent(Container.java:2041)
at java.awt.Component.dispatchEventImpl(Component.java:4630)
at java.awt.Container.dispatchEventImpl(Container.java:2099)
at java.awt.Component.dispatchEvent(Component.java:4460)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
at java.awt.Container.dispatchEventImpl(Container.java:2085)
at java.awt.Component.dispatchEvent(Component.java:4460)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:125)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
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Application freeze when importing graph file on Linux.
Way to reproduce:
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logfile attached
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Error on loading the file attached :
java.lang.ArrayIndexOutOfBoundsException: 65539
at gephi.io.fileformat.GephiReader.readWorkSpace(GephiReader.java:190)
at gephi.io.fileformat.GephiReader.readProject(GephiReader.java:122)
at gephi.io.fileformat.GephiReader.readEverything(GephiReader.java:86)
at gephi.io.ProjectFileRecorder$ProjectInputStream.readProject(ProjectFileRecorder.java:264)
at gephi.io.ProjectFileRecorder.readProject(ProjectFileRecorder.java:87)
at gephi.io.ProjectFileRecorder.readProject(ProjectFileRecorder.java:111)
at gephi.controller.desktop.DesktopProjectController$2.run(DesktopProjectController.java:215)
at java.lang.Thread.run(Thread.java:619)
Exception in thread "Thread-9" java.lang.NullPointerException
at gephi.controller.desktop.DesktopProjectController$2.run(DesktopProjectController.java:216)
at java.lang.Thread.run(Thread.java:619)
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I have made several graphs from gdf files and am using Topology > Degree Range Filter and Relative Node Size text labels, however saving these projects never retain the information. Kinda annoying to set this up everytime, apart from that awesome software!
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Menubar is incomplete and don't show all elements.
Problem has been reported on Mac OS X.
http://forum.gephi.org/viewtopic.php?f=4&t=64
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Hi,
this looks like a pretty annoying bug:
I'm working with dynamic timeline data, which exists in the first place as a GEXF file (sample attached to this bug report). After loading the GEXF file, I can click on the timeline 'play' button, and the timeline slider works as expected - in the case of the data I work with, network edges appear and disappear as I use the slider. (In my data, only edges have timeline information - nodes are always visible.)
If I save this project as a .gephi file and reload the project file, however, the timeline functionality no longer works, and there doesn't seem to be any way to get it back. Any way to fix this ?
I'm attaching a GEXF data file so you can reproduce this issue. Here are the steps:
Many thanks in advance,
Axel Bruns
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This bug appears in alpha4 when importing any dynamic graph
Stack trace:
Caused by: java.lang.NullPointerException
at org.gephi.desktop.timeline.TimelineControllerImpl.pushSlice(TimelineControllerImpl.java:107)
at org.gephi.desktop.timeline.TimelineControllerImpl.pushSlice(TimelineControllerImpl.java:355)
at org.gephi.io.processor.plugin.AbstractProcessor.flushToNode(AbstractProcessor.java:81)
at org.gephi.io.processor.plugin.DefaultProcessor.process(DefaultProcessor.java:99)
at org.gephi.io.importer.impl.ImportControllerImpl.process(ImportControllerImpl.java:144)
at org.gephi.desktop.importer.DesktopImportControllerUI.finishImport(DesktopImportControllerUI.java:233)
at org.gephi.desktop.importer.DesktopImportControllerUI.access$100(DesktopImportControllerUI.java:46)
at org.gephi.desktop.importer.DesktopImportControllerUI$2.run(DesktopImportControllerUI.java:102)
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This bug affects certain configuration only.
The problem seems to be related to gluegen library. The current gluegen is from JOGL 1.1.1a
Stack trace:
java.lang.RuntimeException: Please port CPU detection (32/64 bit) to your platform (mac os x/x86_64)
at com.sun.gluegen.runtime.CPU.(CPU.java:72)
Caused: java.lang.ExceptionInInitializerError
at com.sun.opengl.impl.JAWT.size(JAWT.java:17)
at com.sun.opengl.impl.JAWT.create(JAWT.java:25)
at com.sun.opengl.impl.JAWT$1.run(JAWT.java:97)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.opengl.impl.JAWT.getJAWT(JAWT.java:95)
at com.sun.opengl.impl.macosx.MacOSXOnscreenGLDrawable.lockSurface(MacOSXOnscreenGLDrawable.java:144)
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.maybeDoSingleThreadedWorkaround(GLCanvas.java:265)
at javax.media.opengl.GLCanvas.display(GLCanvas.java:130)
at javax.media.opengl.GLCanvas.paint(GLCanvas.java:142)
at sun.awt.RepaintArea.paintComponent(RepaintArea.java:276)
at sun.awt.RepaintArea.paint(RepaintArea.java:241)
at apple.awt.ComponentModel.handleEvent(ComponentModel.java:263)
at java.awt.Component.dispatchEventImpl(Component.java:4790)
at java.awt.Component.dispatchEvent(Component.java:4544)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:635)
at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:125)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
[catch] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
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According to mbastian: "Yes I confirm, there is a bug, no graph is shown until there is some edges in the graph."
See: http://forum.gephi.org/viewtopic.php?f=8&t=33
Way to reproduce:
The problem also appears if imported (or generated) data contains no edges
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Hierarchy not imported.
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Way to reproduce:
Stack trace:
java.lang.NullPointerException
at org.gephi.visualization.opengl.octree.Octree.removeObject(Octree.java:121)
at org.gephi.visualization.opengl.octree.Octree.cleanDeletedObjects(Octree.java:236)
at org.gephi.visualization.opengl.compatibility.CompatibilityEngine.worldUpdated(CompatibilityEngine.java:199)
at org.gephi.visualization.bridge.DHNSDataBridge.updateWorld(DHNSDataBridge.java:145)
at org.gephi.visualization.opengl.compatibility.CompatibilityEngine.updateWorld(CompatibilityEngine.java:181)
at org.gephi.visualization.opengl.compatibility.CompatibilityScheduler.updateWorld(CompatibilityScheduler.java:270)
at org.gephi.visualization.scheduler.SimpleFPSAnimator.run(SimpleFPSAnimator.java:57)
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java.lang.NullPointerException
at org.gephi.visualization.opengl.compatibility.objects.Arrow2dModel.isInOctreeLeaf(Arrow2dModel.java:199)
at org.gephi.visualization.opengl.octree.Octree.updateObjectsPosition(Octree.java:268)
at org.gephi.visualization.opengl.compatibility.CompatibilityEngine.updateObjectsPosition(CompatibilityEngine.java:636)
at org.gephi.visualization.opengl.compatibility.CompatibilityScheduler.updatePosition(CompatibilityScheduler.java:279)
[catch] at org.gephi.visualization.scheduler.SimpleFPSAnimator.run(SimpleFPSAnimator.java:58)
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Way to reproduce:
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Hello,
I've installed Gephi-0.7 on a Mac OS X v 10.5.8.
When I run the software I only obtain a short menu: GephiDesktop and no other functions.
I can correctly used this same software on my PC Windows.
I thank you by advance
Best resgards
Bénédicte B.
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Stack trace:
java.lang.Error: Maximum lock count exceeded
at java.util.concurrent.locks.ReentrantReadWriteLock$Sync.tryAcquireShared(ReentrantReadWriteLock.java:395)
at java.util.concurrent.locks.AbstractQueuedSynchronizer.acquireShared(AbstractQueuedSynchronizer.java:1260)
at java.util.concurrent.locks.ReentrantReadWriteLock$ReadLock.lock(ReentrantReadWriteLock.java:594)
at org.gephi.graph.dhns.core.Dhns.readLock(Dhns.java:166)
at org.gephi.graph.dhns.graph.AbstractGraphImpl.readLock(AbstractGraphImpl.java:65)
at org.gephi.visualization.bridge.DHNSDataBridge.updateWorld(DHNSDataBridge.java:118)
at org.gephi.visualization.opengl.compatibility.CompatibilityEngine.updateWorld(CompatibilityEngine.java:181)
at org.gephi.visualization.opengl.compatibility.CompatibilityScheduler.updateWorld(CompatibilityScheduler.java:285)
at org.gephi.visualization.scheduler.SimpleFPSAnimator.run(SimpleFPSAnimator.java:58)
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Way to reproduce here: http://forum.gephi.org/viewtopic.php?f=4&t=395
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The process don't stop when I try to cancel the opening of the attached project. Btw, I can't load it completely even if there is enough memory.
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Steps to reproduce:
If I delete half of the edges, the problem doesn't appear anymore.
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OS: Windows 7 64 bits
Version: Gephi 0.7a4
Gephi does not launch at all. It was installed using a local admin account. Trying to run gephidesktop.exe results in the following error:
"Your user directory (C:\Program Files (x86)\Gephi-0.7) cannot reside inside your NetBeans installation directory (C:\Program Files (x86)\Gephi-0.7)."
Environment parameters:
HOMEDRIVE=C:
HOMEPATH=\Users\raynorvliegendhart
Workaround:
Change default_userdir in gephidesktop.conf from "${HOME}/.${APPNAME}/dev" to the hardcoded path "c:/Users/raynorvliegendhart/".
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Preview module doesn't take in account filtering and displays nodes that are hidden by filtering.
Way to reproduce:
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This bug concerns only Gephi 0.6beta2.
On linux desktop installation or running online demo the SVG Export panel is not functioning.
Reproduce this bug:
Nothing happens after that, and the exception is hidden. It appears only in console.
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Banner bar, which let users choose between "Overview", "Data Laboratory" or "Preview" doesn't show on Mac OS X and Linux.
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After closing Layout Window, it is impossible to open it again, from the Window menu or by restarting program.
Way to reproduce:
A workaround is to clean user directory, when Gephi is turned off:
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