Update disabled, hangs Gephi

[Rodger22]

Dear Experts,

I'm running Gephi on Redhat 6.4.

lsb_release -a
LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: OracleServer
Description: Oracle Linux Server release 6.4
Release: 6.4
Codename: n/a


uname -a
Linux black.testrac.com 2.6.32-358.11.1.el6.x86_64 #1 SMP Tue Jun 11 10:24:58 PDT 2013 x86_64 x86_64 x86_64 GNU/Linux


env | grep -i "java"
JAVA_PATH=/usr/java/jre1.7.0_21/bin
JAVA_HOME=/usr/java/jre1.7.0_21


---------


I've been having some serious issues with tools, updates.

When I go to update Gephi, the update window comes up.
But the window is completely disabled.
Clicking the close or help button does nothing.
Then, Gephi is completely disabled.
Although, I can move the update window around.


---

I've then had to go into a console window and kill the two gephi processes.

ps -ef | grep -i "gephi"

oracle 4423 3884 0 14:37 pts/1 00:00:00 /bin/bash ./../platform/lib/nbexec --jdkhome --clusters ./../gephi:./../platform: --userdir /home/oracle/.gephi/0.8.2/dev --branding gephi -J-Xms64m -J-Xmx11165m -J-Xverify:none -J-Dsun.java2d.noddraw=true -J-Dsun.awt.noerasebackground=true -J-Dnetbeans.indexing.noFileRefresh=true -J-Dplugin.manager.check.interval=EVERY_DAY

oracle 4798 4423 35 14:37 pts/1 00:00:32 /usr/lib/jvm/java-1.7.0-openjdk.x86_64/bin/java -Djdk.home=/usr/lib/jvm/java-1.7.0-openjdk.x86_64 -classpath /gephi/gephi/platform/lib/boot.jar:/gephi/gephi/platform/lib/org-openide-modules.jar:/gephi/gephi/platform/lib/org-openide-util.jar:/gephi/gephi/platform/lib/org-openide-util-lookup.jar:/gephi/gephi/platform/lib/locale/boot_ar_SA.jar:/gephi/gephi/platform/lib/locale/boot_bg.jar:/gephi/gephi/platform/lib/locale/boot_ca.jar:/gephi/gephi/platform/lib/locale/boot_cs.jar:/gephi/gephi/platform/lib/locale/boot_de.jar:/gephi/gephi/platform/lib/locale/boot_es.jar:/gephi/gephi
...


-----------



When this happened a few weeks ago, the following seemed to work:

Go into the user's subdirectory for gephi, and delete all the files.

cd /home/oracle/.gephi/0.8.2
rm -vrf *

These subdirectories seem to be for preferences, etc.

After doing that, the update worked.

But doing the same thing today, did not help.
Even after rebooting the server.


Any ideas? I don't want to spend another week doing a deep dive to
get the tool to work.



Best,


Rodger

[Rodger22]

Ok, here is an update with lots of debug information.


I uninstalled gephi, deleting everything from the subdirectory.
And deleted everything from the directory: /home/user/.gephi

----

Gephi boots. Start installing plugins.

Installed:
91 plugins


Available:

2 updates
38 plugins


Install updates 5 to 10 at a time and reboot.

Get a few dozen installed.
Reboot each time.


Then the fifth time I boot Gephi, when I open the plugin, I get the same disabled symptom.

-----------------


Points I note:


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


However, netbeans is not installed on my server.

rpm -qa | grep -i "netbe"
- nothing



How can netbeans.default_userdir_root be set in Gephi?


-----


Details from the logs are below.


It took about 2 hours to compile this info.
Gephi Java developers, please review.


-----------


cd /gephi/gephi/gephi/config/Modules


ls -lrt

...
-rwxr-xr-x. 1 oracle dba 477 Jan 3 2013 org-gephi-clustering-plugin.xml
-rwxr-xr-x. 1 oracle dba 479 Jan 3 2013 org-gephi-ui-library-wrapper.xml
-rw-r--r--. 1 oracle dba 463 Aug 5 10:44 org-gephi-attributes.xml
-rw-r--r--. 1 oracle dba 463 Aug 5 10:44 org-gephi-db-drivers.xml
-rw-r--r--. 1 oracle dba 459 Aug 5 10:45 org-gephi-desktop-neo4j.xml
-rw-r--r--. 1 oracle dba 457 Aug 5 10:45 org-gephi-neo4j-plugin.xml
-rw-r--r--. 1 oracle dba 411 Aug 5 10:45 org-gephi-lib-neo4j.xml
-rw-r--r--. 1 oracle dba 443 Aug 5 10:45 org-gephi-neo4j.xml
-rw-r--r--. 1 oracle dba 467 Aug 5 10:45 org-gephi-desktop-streaming.xml
-rw-r--r--. 1 oracle dba 503 Aug 5 10:45 umberto-G_TruncatedLevyWalkMobilityModel.xml
-rw-r--r--. 1 oracle dba 459 Aug 5 10:45 org-gephi-streaming-api.xml
-rw-r--r--. 1 oracle dba 465 Aug 5 10:45 org-liborm-CCDisjoint.xml
-rw-r--r--. 1 oracle dba 461 Aug 5 10:45 org-gephi-graphstreaming.xml
-rw-r--r--. 1 oracle dba 491 Aug 5 10:45 umberto-MobilitySimulatorInterface.xml
-rw-r--r--. 1 oracle dba 465 Aug 5 10:45 org-gephi-streaming-server.xml
-rw-r--r--. 1 oracle dba 461 Aug 5 10:45 org-gephi-streaming-impl.xml
-rw-r--r--. 1 oracle dba 451 Aug 5 10:45 org-gephi-lib-jetty.xml
-rw-r--r--. 1 oracle dba 495 Aug 5 10:46 org-gephi-io-complexgenerator-plugin.xml
-rw-r--r--. 1 oracle dba 491 Aug 5 10:46 umberto-WeightedClusterCoefficient.xml
-rw-r--r--. 1 oracle dba 413 Aug 5 10:46 org-gephi-lib-gython.xml
-rw-r--r--. 1 oracle dba 455 Aug 5 10:46 org-vijesh-concentric.xml
-rw-r--r--. 1 oracle dba 477 Aug 5 10:46 org-gephi-complexgenerators.xml
-rw-r--r--. 1 oracle dba 469 Aug 5 10:46 org-gephi-plugins-layout-geo.xml
-rw-r--r--. 1 oracle dba 451 Aug 5 10:46 org-gephi-scripting.xml
-rw-r--r--. 1 oracle dba 495 Aug 5 10:46 org-gephi-ui-complexgenerator-plugin.xml


No linkfluence here.

-------------------

Here are some info from the logs:



cat /home/oracle/.gephi/0.8.2/dev/var/log/updater.log.0

...
Aug 05, 2013 10:46:59 AM org.netbeans.updater.ModuleUpdater unpack200
INFO: Unpack /home/oracle/.gephi/0.8.2/dev/modules/uk-ac-ox-oii-jsonexporter.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/uk-ac-ox-oii-jsonexporter.jar
Aug 05, 2013 10:46:59 AM org.netbeans.updater.ModuleUpdater unpack
INFO: File /home/oracle/.gephi/0.8.2/dev/modules/uk-ac-ox-oii-jsonexporter.jar.pack.gz deleted.
Aug 05, 2013 10:46:59 AM org.netbeans.updater.ModuleUpdater unpack
INFO: File /home/oracle/.gephi/0.8.2/dev/update/download/uk-ac-ox-oii-jsonexporter.nbm deleted.
Aug 05, 2013 10:46:59 AM org.netbeans.updater.XMLUtil write
INFO: Use XML Transformer: com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl@562962ff
Aug 05, 2013 10:46:59 AM org.netbeans.updater.UpdateTracking$Module write
INFO: File /home/oracle/.gephi/0.8.2/dev/update_tracking/uk-ac-ox-oii-jsonexporter.xml modified.
Aug 05, 2013 10:46:59 AM org.netbeans.updater.ModuleUpdater unpack
INFO: Copied file netbeans/config/Modules/org-gephi-linkfluence.xml to /home/oracle/.gephi/0.8.2/dev/config/Modules/org-gephi-linkfluence.xml
Aug 05, 2013 10:46:59 AM org.netbeans.updater.ModuleUpdater unpack
INFO: Copied file netbeans/modules/org-gephi-linkfluence.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/org-gephi-linkfluence.jar.pack.gz
Aug 05, 2013 10:46:59 AM org.netbeans.updater.ModuleUpdater unpack200
INFO: Unpack /home/oracle/.gephi/0.8.2/dev/modules/org-gephi-linkfluence.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/org-gephi-linkfluence.jar
Aug 05, 2013 10:46:59 AM org.netbeans.updater.ModuleUpdater unpack
INFO: File /home/oracle/.gephi/0.8.2/dev/modules/org-gephi-linkfluence.jar.pack.gz deleted.
Aug 05, 2013 10:46:59 AM org.netbeans.updater.ModuleUpdater unpack
INFO: File /home/oracle/.gephi/0.8.2/dev/update/download/org-gephi-linkfluence.nbm deleted.
Aug 05, 2013 10:46:59 AM org.netbeans.updater.XMLUtil write
INFO: Use XML Transformer: com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl@27af9da2
Aug 05, 2013 10:46:59 AM org.netbeans.updater.UpdateTracking$Module write
INFO: File /home/oracle/.gephi/0.8.2/dev/update_tracking/org-gephi-linkfluence.xml modified.
Aug 05, 2013 10:46:59 AM org.netbeans.updater.ModuleUpdater deleteAdditionalInfo
INFO: File /home/oracle/.gephi/0.8.2/dev/update/download/additional_information.xml deleted.
Aug 05, 2013 10:46:59 AM org.netbeans.updater.ModuleUpdater deleteAdditionalInfo
INFO: File ./../gephi/update/download/additional_information.xml deleted.





It seemed to be working on linkfluence, then crashed.



------------------------

messages.log


grep -i -e "updat" -i -e "instal" -i -e "upgrad" -i -e "import" -i -e "warn" -i -e "sever" -i -e "info" /home/oracle/.gephi/0.8.2/dev/var/log/messages.log


>System Info:
Installation = /gephi/gephi/gephi
WARNING [org.netbeans.core.modules]: had to upgrade dependencies for module org.icculus.chunky.gephigraphviz: added = [module org.openide.awt] removed = []; details: [SaveCookie extends Savable. To compile you need to include openide.awt on classpath.]
WARNING [org.netbeans.core.startup.NbEvents]: The extension /home/oracle/.gephi/0.8.2/dev/modules/ext/commons-logging-1.1.1.jar may be multiply loaded by modules: [/home/oracle/.gephi/0.8.2/dev/modules/fr-inria-edelweiss-semantic.jar, /home/oracle/.gephi/0.8.2/dev/modules/net-phreakocious-httpgraph.jar]; see: http://www.netbeans.org/download/dev/ja ... class-path
WARNING [org.netbeans.core.startup.NbEvents]: The extension /home/oracle/.gephi/0.8.2/dev/modules/ext/activation-1.1.jar may be multiply loaded by modules: [/home/oracle/.gephi/0.8.2/dev/modules/fr-inria-edelweiss-semantic.jar, /home/oracle/.gephi/0.8.2/dev/modules/net-phreakocious-httpgraph.jar]; see: http://www.netbeans.org/download/dev/ja ... class-path
WARNING [org.netbeans.core.startup.NbEvents]: The extension /gephi/gephi/gephi/modules/ext/fastutil-6.4.4.jar may be multiply loaded by modules: [/gephi/gephi/gephi/modules/umberto-MobilitySimulatorInterface.jar, /gephi/gephi/gephi/modules/umberto-G_TruncatedLevyWalkMobilityModel.jar]; see: http://www.netbeans.org/download/dev/ja ... class-path
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/gephi/gephi/gephi/modules/org-gephi-io-complexgenerator-plugin.jar!/org/gephi/io/complexgenerator/plugin/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/gephi/gephi/gephi/modules/org-gephi-streaming-api.jar!/org/gephi/streaming/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/gephi/gephi/gephi/modules/org-gephi-streaming-server.jar!/org/gephi/streaming/server/layer.xml


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



SEVERE [org.netbeans.core.modules]
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings.getSuperIdentity(AutoupdateSettings.java:435)
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings.generateIdentity(AutoupdateSettings.java:136)
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateCheckScheduler.signOn(AutoupdateCheckScheduler.java:110)
at org.netbeans.modules.autoupdate.ui.actions.Installer.restored(Installer.java:63)
at org.netbeans.core.startup.NbInstaller.loadCode(NbInstaller.java:469)
[catch] at org.netbeans.core.startup.NbInstaller.loadImpl(NbInstaller.java:392)
at org.netbeans.core.startup.NbInstaller.access$000(NbInstaller.java:103)
at org.netbeans.core.startup.NbInstaller$1.run(NbInstaller.java:344)
at org.netbeans.core.startup.NbInstaller.load(NbInstaller.java:341)
at org.netbeans.core.startup.ModuleList.installNew(ModuleList.java:340)
INFO [org.netbeans.core.startup.NbEvents]: Turning on modules:
org.gephi.io.importer.api [0.8.2 0.8.2 201301031859]
org.netbeans.modules.autoupdate.services [1.33.2 201210100934]
org.netbeans.modules.autoupdate.ui [1.27.3 201210100934]
org.gephi.settings.upgrader [0.8.2 0.8.2 201301031900]
org.gephi.io.importer.plugin [0.8.2 0.8.2 201301031905]
org.gephi.import.plugin.ui [0.8.2 0.8.2 201301031906]
org.gephi.desktop.import [0.8.2 0.8.2 201301031907]
de.uni_leipzig.informatik.asv.gephi.chinesewhispers/0 [0.3 120821]
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: dirURL = file:/home/oracle/.gephi/0.8.2/dev/modules/fr-inria-edelweiss-semantic.jar!/fr/inria/edelweiss/semantic/default_configuration/, protocol = jar
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: META-INF/
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: META-INF/MANIFEST.MF
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: META-INF/services/
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: fr/
...

INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: fr/inria/wimmics/semanticweb/filter/type/TypeFilterPanel.class
WARNING [org.netbeans.TopSecurityManager]: use of system property netbeans.user has been obsoleted in favor of InstalledFileLocator/Places at org.gephi.ui.upgrader.Upgrader.getCurrentVersion(Upgrader.java:123)
Diagnostic information
INFO [org.netbeans.core.ui.warmup.DiagnosticTask]: Total memory 16,724,840,448
INFO [null]: Total physical memory 16,724,840,448
WARNING [org.openide.filesystems.Ordering]: Found same position 600 for both Menu/File/org-gephi-desktop-importer-ImportDB.instance and Menu/File/org-gephi-desktop-neo4j-Neo4jMenuAction.instance
WARNING [org.openide.filesystems.Ordering]: Not all children in Menu/Window/ marked with the position attribute: [fr-inria-edelweiss-SemanticWebImportMainWindowTopComponent.shadow], but some are: [org-gephi-desktop-clustering-ClusteringTopComponent.shadow, org-gephi-desktop-clustering-ContextTopComponent.shadow, org-gephi-desktop-datalab-DataTableTopComponent.shadow, org-gephi-desktop-filters-FiltersTopComponent.shadow, org-gephi-visualization-component-GraphTopComponent.shadow, org-gephi-desktop-datalab-HierarchyTopComponent.shadow, org-gephi-desktop-layout-LayoutTopComponent.shadow, org-gephi-desktop-partition-PartitionTopComponent.shadow, org-gephi-desktop-preview-PreviewTopComponent.shadow, org-gephi-desktop-preview-PreviewSettingsTopComponent.shadow, org-gephi-desktop-ranking-RankingTopComponent.shadow, org-gephi-desktop-welcome-WelcomeAction.shadow, org-gephi-desktop-statistics-StatisticsTopComponent.shadow, org-gephi-desktop-timeline-TimelineWindowAction.shadow, org-gephi-desktop-streaming-StreamingTopComponent.shadow, Separator3.instance, ConfigureWindow, Separator4.instance, CloseWindowAction.shadow, Separator4_1.instance]
WARNING [org.netbeans.modules.autoupdate.updateproviders.AutoupdateCatalogFactory]: Services/AutoupdateType/org_gephi_branding_update_center.instance: url_key attribute deprecated in favor of url


-------------------------

messages.log.1


/home/oracle/.gephi/0.8.2/dev/var/log/messages.log.1


grep -i -e "updat" -i -e "instal" -i -e "upgrad" -i -e "import" -i -e "warn" -i -e "sever" -i -e "info" /home/oracle/.gephi/0.8.2/dev/var/log/messages.log.1

>System Info:
Installation = /gephi/gephi/gephi
WARNING [org.netbeans.core.startup.NbEvents]: The extension /gephi/gephi/gephi/modules/ext/fastutil-6.4.4.jar may be multiply loaded by modules: [/gephi/gephi/gephi/modules/umberto-MobilitySimulatorInterface.jar, /gephi/gephi/gephi/modules/umberto-G_TruncatedLevyWalkMobilityModel.jar]; see: http://www.netbeans.org/download/dev/ja ... class-path
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/gephi/gephi/gephi/modules/org-gephi-streaming-api.jar!/org/gephi/streaming/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/gephi/gephi/gephi/modules/org-gephi-streaming-server.jar!/org/gephi/streaming/server/layer.xml

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


SEVERE [org.netbeans.core.modules]
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings.getSuperIdentity(AutoupdateSettings.java:435)
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings.generateIdentity(AutoupdateSettings.java:136)
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateCheckScheduler.signOn(AutoupdateCheckScheduler.java:110)
at org.netbeans.modules.autoupdate.ui.actions.Installer.restored(Installer.java:63)
at org.netbeans.core.startup.NbInstaller.loadCode(NbInstaller.java:469)
[catch] at org.netbeans.core.startup.NbInstaller.loadImpl(NbInstaller.java:392)
at org.netbeans.core.startup.NbInstaller.access$000(NbInstaller.java:103)
at org.netbeans.core.startup.NbInstaller$1.run(NbInstaller.java:344)
at org.netbeans.core.startup.NbInstaller.load(NbInstaller.java:341)
at org.netbeans.core.startup.ModuleList.installNew(ModuleList.java:340)
INFO [org.netbeans.core.startup.NbEvents]: Turning on modules:
org.gephi.io.importer.api [0.8.2 0.8.2 201301031859]
org.netbeans.modules.autoupdate.services [1.33.2 201210100934]
org.netbeans.modules.autoupdate.ui [1.27.3 201210100934]
org.gephi.settings.upgrader [0.8.2 0.8.2 201301031900]
org.gephi.io.importer.plugin [0.8.2 0.8.2 201301031905]
org.gephi.import.plugin.ui [0.8.2 0.8.2 201301031906]
org.gephi.desktop.import [0.8.2 0.8.2 201301031907]
de.uni_leipzig.informatik.asv.gephi.chinesewhispers/0 [0.3 120821]
WARNING [org.netbeans.TopSecurityManager]: use of system property netbeans.user has been obsoleted in favor of InstalledFileLocator/Places at org.gephi.ui.upgrader.Upgrader.getCurrentVersion(Upgrader.java:123)
Diagnostic information
INFO [org.netbeans.core.ui.warmup.DiagnosticTask]: Total memory 16,724,840,448
INFO [null]: Total physical memory 16,724,840,448
WARNING [org.openide.filesystems.Ordering]: Found same position 600 for both Menu/File/org-gephi-desktop-importer-ImportDB.instance and Menu/File/org-gephi-desktop-neo4j-Neo4jMenuAction.instance
WARNING [org.netbeans.modules.autoupdate.updateproviders.AutoupdateCatalogFactory]: Services/AutoupdateType/org_gephi_branding_update_center.instance: url_key attribute deprecated in favor of url
WARNING [org.netbeans.modules.autoupdate.updateproviders.AutoupdateCatalogFactory]: Services/AutoupdateType/org_gephi_branding_update_center_1.instance: url_key attribute deprecated in favor of url
WARNING [org.netbeans.modules.autoupdate.services.Utilities]: had to upgrade dependencies for module org.icculus.chunky.gephigraphviz: added = [module org.openide.awt] removed = []; details: [SaveCookie extends Savable. To compile you need to include openide.awt on classpath.]
WARNING [org.netbeans.modules.autoupdate.services.Utilities]: had to upgrade dependencies for module org.icculus.chunky.gephigraphviz: added = [module org.openide.awt] removed = []; details: [SaveCookie extends Savable. To compile you need to include openide.awt on classpath.]
WARNING [org.netbeans.modules.autoupdate.services.Utilities]: had to upgrade dependencies for module org.icculus.chunky.gephigraphviz: added = [module org.openide.awt] removed = []; details: [SaveCookie extends Savable. To compile you need to include openide.awt on classpath.]
WARNING [org.netbeans.modules.autoupdate.services.Utilities]: had to upgrade dependencies for module org.icculus.chunky.gephigraphviz: added = [module org.openide.awt] removed = []; details: [SaveCookie extends Savable. To compile you need to include openide.awt on classpath.]







-------------------------

messages.log.2

/home/oracle/.gephi/0.8.2/dev/var/log/messages.log.2

grep -i -e "updat" -i -e "instal" -i -e "upgrad" -i -e "import" -i -e "warn" -i -e "sever" -i -e "info" /home/oracle/.gephi/0.8.2/dev/var/log/messages.log.2

>System Info:
Installation = /gephi/gephi/gephi
WARNING [org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings]: The property "netbeans.default_userdir_root" was not set!
WARNING [org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings]: The property "netbeans.default_userdir_root" was not set!
SEVERE [org.netbeans.core.modules]
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings.getSuperIdentity(AutoupdateSettings.java:435)
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings.generateIdentity(AutoupdateSettings.java:136)
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateCheckScheduler.signOn(AutoupdateCheckScheduler.java:110)
at org.netbeans.modules.autoupdate.ui.actions.Installer.restored(Installer.java:63)
at org.netbeans.core.startup.NbInstaller.loadCode(NbInstaller.java:469)
[catch] at org.netbeans.core.startup.NbInstaller.loadImpl(NbInstaller.java:392)
at org.netbeans.core.startup.NbInstaller.access$000(NbInstaller.java:103)
at org.netbeans.core.startup.NbInstaller$1.run(NbInstaller.java:344)
at org.netbeans.core.startup.NbInstaller.load(NbInstaller.java:341)
at org.netbeans.core.startup.ModuleList.installNew(ModuleList.java:340)
INFO [org.netbeans.core.startup.NbEvents]: Turning on modules:
org.netbeans.modules.autoupdate.services [1.33.2 201210100934]
org.netbeans.modules.autoupdate.ui [1.27.3 201210100934]
org.gephi.io.importer.api [0.8.2 0.8.2 201301031859]
org.gephi.settings.upgrader [0.8.2 0.8.2 201301031900]
org.gephi.io.importer.plugin [0.8.2 0.8.2 201301031905]
org.gephi.import.plugin.ui [0.8.2 0.8.2 201301031906]
org.gephi.desktop.import [0.8.2 0.8.2 201301031907]
WARNING [org.netbeans.TopSecurityManager]: use of system property netbeans.user has been obsoleted in favor of InstalledFileLocator/Places at org.gephi.ui.upgrader.Upgrader.getCurrentVersion(Upgrader.java:123)
Diagnostic information
INFO [org.netbeans.core.ui.warmup.DiagnosticTask]: Total memory 16,724,840,448
INFO [null]: Total physical memory 16,724,840,448
WARNING [org.openide.filesystems.Ordering]: Found same position 600 for both Menu/File/org-gephi-desktop-importer-ImportDB.instance and Menu/File/org-gephi-desktop-neo4j-Neo4jMenuAction.instance
WARNING [org.netbeans.modules.autoupdate.updateproviders.AutoupdateCatalogFactory]: Services/AutoupdateType/org_gephi_branding_update_center.instance: url_key attribute deprecated in favor of url
WARNING [org.netbeans.modules.autoupdate.updateproviders.AutoupdateCatalogFactory]: Services/AutoupdateType/org_gephi_branding_update_center_1.instance: url_key attribute deprecated in favor of url



----------------



Any ideas?

[francis_flavin]

Hi Rodger,

A short time ago I had trouble with Gephi's updater seeming to hang. I presumed that it was a connectivity problem or that the plug-in server was down and I didn't spend much time looking into it. I'll be on the lookout for this problem again and, if it happens, I'll dig a little deeper. I'm running on both Windows 7 and Windows 8, btw.

Good luck and thanks for the post!

Francis

[Rodger22]

Ok, there is the feature to upload an image.

Here is what the screen looks like when it is disabled.

When this happens, neither button, Close or Help works.
I can move the window around the Gephi screen.

Then, I have to use the kill command on Gephi and restart it.

[raz2raz]

I have this same behavior in Win 7.. any updates?

[Rodger22]

Hello all,

Well, it happened again.

On Redhat 6.4, as a non-root unix user, I went
to install a number of new plugins today.
And now I have the same symptoms. Again.

I believe that most of the plugins installed.

But some plugin about script(s) gave me trouble.
Is it the culprit?


Interestingly enough, when I start Gephi from root, and the update window is enabled.
And, a whole bunch of plugins that I installed as the other unix user were available to install.

So, clearly, Gephi is installing these, by unix user. Not for all unix users.
This is unlike an RPM package that you install on your server, which is then
available for all users.

I notice that the latest version of Gephi is 082, what was available in the spring.
Is a new release in the works?
Has any work been done on this error?

How do you set: netbeans.default_userdir_root ?

How can this error be dealt with?
SEVERE [org.netbeans.core.modules]
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings.getSuperIdentity(AutoupdateSettings.java:435)


Excerpts follow from messages.log.2:

Thanks a lot,

Rodger




grep -i -e "updat" -i -e "instal" -i -e "upgrad" -i -e "import" -i -e "warn" -i -e "sever" -i -e "info" /home/oracle/.gephi/0.8.2/dev/var/log/messages.log.2
>System Info:


Installation = /gephi/gephi/gephi
WARNING [org.netbeans.core.modules]: had to upgrade dependencies for module org.icculus.chunky.gephigraphviz: added = [module org.openide.awt] removed = []; details: [SaveCookie extends Savable. To compile you need to include openide.awt on classpath.]
WARNING [org.netbeans.core.startup.NbEvents]: The extension /home/oracle/.gephi/0.8.2/dev/modules/ext/commons-logging-1.1.1.jar may be multiply loaded by modules: [/home/oracle/.gephi/0.8.2/dev/modules/fr-inria-edelweiss-semantic.jar, /home/oracle/.gephi/0.8.2/dev/modules/net-phreakocious-httpgraph.jar]; see: http://www.netbeans.org/download/dev/ja ... class-path
WARNING [org.netbeans.core.startup.NbEvents]: The extension /home/oracle/.gephi/0.8.2/dev/modules/ext/activation-1.1.jar may be multiply loaded by modules: [/home/oracle/.gephi/0.8.2/dev/modules/fr-inria-edelweiss-semantic.jar, /home/oracle/.gephi/0.8.2/dev/modules/net-phreakocious-httpgraph.jar]; see: http://www.netbeans.org/download/dev/ja ... class-path
WARNING [org.netbeans.core.modules]: had to upgrade dependencies for module org.gephi.plugins.layout.noverlap: added = [module org.openide.util.lookup > 8.0] removed = []; details: [#170056: Separate module for Lookup API]
WARNING [org.netbeans.core.startup.NbEvents]: The extension /gephi/gephi/gephi/modules/ext/fastutil-6.4.4.jar may be multiply loaded by modules: [/gephi/gephi/gephi/modules/umberto-MobilitySimulatorInterface.jar, /gephi/gephi/gephi/modules/umberto-G_TruncatedLevyWalkMobilityModel.jar, /gephi/gephi/gephi/modules/umberto-G_RandomWaypointMobilityModel.jar]; see: http://www.netbeans.org/download/dev/ja ... class-path
WARNING [org.netbeans.core.startup.NbEvents]: The extension /gephi/gephi/gephi/modules/ext/fastutil-6.4.4.jar may be multiply loaded by modules: [/gephi/gephi/gephi/modules/umberto-MobilitySimulatorInterface.jar, /gephi/gephi/gephi/modules/umberto-G_TruncatedLevyWalkMobilityModel.jar, /gephi/gephi/gephi/modules/umberto-G_RandomWaypointMobilityModel.jar]; see: http://www.netbeans.org/download/dev/ja ... class-path
WARNING [org.netbeans.core.modules]: had to upgrade dependencies for module org.gephi.layout.plugin.circularlayout: added = [module org.openide.awt] removed = []; details: [SaveCookie extends Savable. To compile you need to include openide.awt on classpath.]
WARNING [org.netbeans.core.modules]: the modules [com.cna.multipartiteLayout, com.hypercities.exporttoearth, ec.loxa.sna.gephi] 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.)
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/gephi/gephi/gephi/modules/org-gephi-io-complexgenerator-plugin.jar!/org/gephi/io/complexgenerator/plugin/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/gephi/gephi/gephi/modules/org-gephi-streaming-api.jar!/org/gephi/streaming/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/gephi/gephi/gephi/modules/org-gephi-streaming-server.jar!/org/gephi/streaming/server/layer.xml
WARNING [org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings]: The property "netbeans.default_userdir_root" was not set!
WARNING [org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings]: The property "netbeans.default_userdir_root" was not set!
SEVERE [org.netbeans.core.modules]
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings.getSuperIdentity(AutoupdateSettings.java:435)
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings.generateIdentity(AutoupdateSettings.java:136)
at org.netbeans.modules.autoupdate.ui.actions.AutoupdateCheckScheduler.signOn(AutoupdateCheckScheduler.java:110)
at org.netbeans.modules.autoupdate.ui.actions.Installer.restored(Installer.java:63)
at org.netbeans.core.startup.NbInstaller.loadCode(NbInstaller.java:469)
[catch] at org.netbeans.core.startup.NbInstaller.loadImpl(NbInstaller.java:392)
at org.netbeans.core.startup.NbInstaller.access$000(NbInstaller.java:103)
at org.netbeans.core.startup.NbInstaller$1.run(NbInstaller.java:344)
at org.netbeans.core.startup.NbInstaller.load(NbInstaller.java:341)
at org.netbeans.core.startup.ModuleList.installNew(ModuleList.java:340)
INFO [org.netbeans.core.startup.NbEvents]: Turning on modules:
org.gephi.io.importer.api [0.8.2 0.8.2 201301031859]
org.ualberta.virtuosoimporter/1 [1.0 130530]
org.netbeans.modules.autoupdate.services [1.33.2 201210100934]
org.netbeans.modules.autoupdate.ui [1.27.3 201210100934]
org.gephi.settings.upgrader [0.8.2 0.8.2 201301031900]
org.gephi.io.importer.plugin [0.8.2 0.8.2 201301031905]
org.gephi.import.plugin.ui [0.8.2 0.8.2 201301031906]
org.gephi.desktop.import [0.8.2 0.8.2 201301031907]
de.uni_leipzig.informatik.asv.gephi.chinesewhispers/0 [0.3 120821]
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: dirURL = file:/home/oracle/.gephi/0.8.2/dev/modules/fr-inria-edelweiss-semantic.jar!/fr/inria/edelweiss/semantic/default_configuration/, protocol = jar
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: META-INF/
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: META-INF/MANIFEST.MF
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: META-INF/services/
...
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: fr/inria/wimmics/semanticweb/filter/type/TypeFilter.class
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: fr/inria/wimmics/semanticweb/filter/type/TypeFilterBuilder.class
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: fr/inria/wimmics/semanticweb/filter/type/TypeFilterPanel.class
WARNING [org.netbeans.TopSecurityManager]: use of system property netbeans.user has been obsoleted in favor of InstalledFileLocator/Places at org.gephi.ui.upgrader.Upgrader.getCurrentVersion(Upgrader.java:123)
Diagnostic information
INFO [org.netbeans.core.ui.warmup.DiagnosticTask]: Total memory 16,724,840,448
INFO [null]: Total physical memory 16,724,840,448
WARNING [org.openide.filesystems.Ordering]: Found same position 600 for both Menu/File/org-gephi-desktop-importer-ImportDB.instance and Menu/File/org-gephi-desktop-neo4j-Neo4jMenuAction.instance
WARNING [org.openide.filesystems.Ordering]: Not all children in Menu/Window/ marked with the position attribute: [cz-cvut-fit-gephi-multimode-MultiModeWindowTopComponent.shadow, fr-inria-edelweiss-SemanticWebImportMainWindowTopComponent.shadow], but some are: [org-gephi-desktop-clustering-ClusteringTopComponent.shadow, org-gephi-desktop-clustering-ContextTopComponent.shadow, org-gephi-desktop-datalab-DataTableTopComponent.shadow, org-gephi-desktop-scripting-ConsoleTopComponent.shadow, org-gephi-desktop-filters-FiltersTopComponent.shadow, org-gephi-visualization-component-GraphTopComponent.shadow, org-gephi-desktop-datalab-HierarchyTopComponent.shadow, org-gephi-desktop-layout-LayoutTopComponent.shadow, org-gephi-desktop-partition-PartitionTopComponent.shadow, org-gephi-desktop-preview-PreviewTopComponent.shadow, org-gephi-desktop-preview-PreviewSettingsTopComponent.shadow, org-gephi-desktop-ranking-RankingTopComponent.shadow, org-gephi-desktop-welcome-WelcomeAction.shadow, org-gephi-desktop-statistics-StatisticsTopComponent.shadow, org-gephi-desktop-timeline-TimelineWindowAction.shadow, org-gephi-desktop-streaming-StreamingTopComponent.shadow, Separator3.instance, ConfigureWindow, Separator4.instance, CloseWindowAction.shadow, Separator4_1.instance]
WARNING [org.netbeans.ProxyClassLoader]: Will not load class org.apache.xerces.jaxp.datatype.DatatypeFactoryImpl arbitrarily from one of ModuleCL@25b43d0d[org.ualberta.virtuosoimporter] and ModuleCL@3e25065f[fr.inria.edelweiss.semantic] starting from SystemClassLoader[194 modules]; see http://wiki.netbeans.org/DevFaqModuleCCE
WARNING [org.netbeans.TopSecurityManager]: use of system property netbeans.user has been obsoleted in favor of InstalledFileLocator/Places at org.gephi.desktop.scripting.ConsoleTopComponent.newJythonConsole(ConsoleTopComponent.java:164)
WARNING [org.netbeans.modules.autoupdate.updateproviders.AutoupdateCatalogFactory]: Services/AutoupdateType/org_gephi_branding_update_center.instance: url_key attribute deprecated in favor of url

[Rodger22]

I've been contemplating so many software errors lately.

Oracle product installs have really burnt me out over the years, with their
150 page installation documents, that still have errors.

And lately, I've been struggling with open source on Linux.


Instead of using the software, I'm spending hours, just to install it!
Investigating. Putting posts online. Trial and error.
It's really tiring and discouraging.

When I think of it, I really enjoy tools that simply: install and work.


I've detailed lots of info here.

Who can get on to a fix for this?

Thanks a lot!

[Rodger22]

Semantic Web Import seems to be the culprit.

What I did follows:


----------

cd /home/oracle/.gephi/0.8.2

rm -vrf *


----------


cd /gephi/gephi/bin
LIBGL_DEBUG=verbose ./gephi &

22 updates available.


Install:

Hiveplot
MapOfCountries
Force Atlas 3d
Convert Excel and CSV files
HTTP Graph
Clustering chinese Whispers

Restart

When I restart, there is a popup from netbeans.
that it is install NBM files, same name as the update.

Install:
LinkCommunities
restart.


Install:
Semantic Web Import
Restart

Go to Update.
Hangs. I can get the hourglass.
But I can't close anything.

Shutdown with unix kill command.


-----------


tail -100 updater.log.0

...
Nov 24, 2013 11:44:17 PM org.netbeans.updater.ModuleUpdater unpack
INFO: Copied file netbeans/modules/de-uni_leipzig-informatik-asv-gephi-chinesewhispers.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/de-uni_leipzig-informatik-asv-gephi-chinesewhispers.jar.pack.gz
Nov 24, 2013 11:44:17 PM org.netbeans.updater.ModuleUpdater unpack200
INFO: Unpack /home/oracle/.gephi/0.8.2/dev/modules/de-uni_leipzig-informatik-asv-gephi-chinesewhispers.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/de-uni_leipzig-informatik-asv-gephi-chinesewhispers.jar
Nov 24, 2013 11:44:17 PM org.netbeans.updater.ModuleUpdater unpack
INFO: File /home/oracle/.gephi/0.8.2/dev/modules/de-uni_leipzig-informatik-asv-gephi-chinesewhispers.jar.pack.gz deleted.
Nov 24, 2013 11:44:17 PM org.netbeans.updater.ModuleUpdater unpack
INFO: File /home/oracle/.gephi/0.8.2/dev/update/download/de-uni_leipzig-informatik-asv-gephi-chinesewhispers.nbm deleted.
Nov 24, 2013 11:44:17 PM org.netbeans.updater.XMLUtil write
INFO: Use XML Transformer: com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl@2da8c7c1
Nov 24, 2013 11:44:17 PM org.netbeans.updater.UpdateTracking$Module write
INFO: File /home/oracle/.gephi/0.8.2/dev/update_tracking/de-uni_leipzig-informatik-asv-gephi-chinesewhispers.xml modified.
Nov 24, 2013 11:44:17 PM org.netbeans.updater.ModuleUpdater unpack
INFO: Copied file netbeans/config/Modules/net-clementlevallois.xml to /home/oracle/.gephi/0.8.2/dev/config/Modules/net-clementlevallois.xml
Nov 24, 2013 11:44:17 PM org.netbeans.updater.ModuleUpdater unpack
INFO: Copied file netbeans/modules/net-clementlevallois.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/net-clementlevallois.jar.pack.gz
Nov 24, 2013 11:44:17 PM org.netbeans.updater.ModuleUpdater unpack200
INFO: Unpack /home/oracle/.gephi/0.8.2/dev/modules/net-clementlevallois.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/net-clementlevallois.jar
Nov 24, 2013 11:44:17 PM org.netbeans.updater.ModuleUpdater unpack
INFO: File /home/oracle/.gephi/0.8.2/dev/modules/net-clementlevallois.jar.pack.gz deleted.
Nov 24, 2013 11:44:17 PM org.netbeans.updater.ModuleUpdater unpack
INFO: File /home/oracle/.gephi/0.8.2/dev/update/download/net-clementlevallois.nbm deleted.
Nov 24, 2013 11:44:17 PM org.netbeans.updater.XMLUtil write
INFO: Use XML Transformer: com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl@7df766ae
Nov 24, 2013 11:44:17 PM org.netbeans.updater.UpdateTracking$Module write
INFO: File /home/oracle/.gephi/0.8.2/dev/update_tracking/net-clementlevallois.xml modified.
Nov 24, 2013 11:44:17 PM org.netbeans.updater.ModuleUpdater deleteAdditionalInfo
INFO: File /home/oracle/.gephi/0.8.2/dev/update/download/additional_information.xml deleted.


----------

tail -500 messages.log.1

....

1.5.11.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/ext/slf4j-log4j12-1.5.11.jar
INFO [org.netbeans.updater]: File /home/oracle/.gephi/0.8.2/dev/modules/ext/slf4j-log4j12-1.5.11.jar.pack.gz deleted.
INFO [org.netbeans.updater]: File installed /home/oracle/.gephi/0.8.2/dev/modules/ext/sparql-1.0.7.jar.pack.gz@0
INFO [org.netbeans.updater]: Copied file netbeans/modules/ext/sparql-1.0.7.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/ext/sparql-1.0.7.jar.pack.gz
INFO [org.netbeans.updater]: Unpack /home/oracle/.gephi/0.8.2/dev/modules/ext/sparql-1.0.7.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/ext/sparql-1.0.7.jar
INFO [org.netbeans.updater]: File /home/oracle/.gephi/0.8.2/dev/modules/ext/sparql-1.0.7.jar.pack.gz deleted.
INFO [org.netbeans.updater]: File installed /home/oracle/.gephi/0.8.2/dev/modules/ext/xercesImpl-2.10.0.jar.pack.gz@0
INFO [org.netbeans.updater]: Copied file netbeans/modules/ext/xercesImpl-2.10.0.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/ext/xercesImpl-2.10.0.jar.pack.gz
INFO [org.netbeans.updater]: Unpack /home/oracle/.gephi/0.8.2/dev/modules/ext/xercesImpl-2.10.0.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/ext/xercesImpl-2.10.0.jar
INFO [org.netbeans.updater]: File /home/oracle/.gephi/0.8.2/dev/modules/ext/xercesImpl-2.10.0.jar.pack.gz deleted.
INFO [org.netbeans.updater]: File installed /home/oracle/.gephi/0.8.2/dev/modules/ext/xml-apis-1.3.03.jar.pack.gz@0
INFO [org.netbeans.updater]: Copied file netbeans/modules/ext/xml-apis-1.3.03.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/ext/xml-apis-1.3.03.jar.pack.gz
INFO [org.netbeans.updater]: Unpack /home/oracle/.gephi/0.8.2/dev/modules/ext/xml-apis-1.3.03.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/ext/xml-apis-1.3.03.jar
INFO [org.netbeans.updater]: File /home/oracle/.gephi/0.8.2/dev/modules/ext/xml-apis-1.3.03.jar.pack.gz deleted.
INFO [org.netbeans.updater]: File installed /home/oracle/.gephi/0.8.2/dev/modules/fr-inria-edelweiss-semantic.jar.pack.gz@0
INFO [org.netbeans.updater]: Copied file netbeans/modules/fr-inria-edelweiss-semantic.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/fr-inria-edelweiss-semantic.jar.pack.gz
INFO [org.netbeans.updater]: Unpack /home/oracle/.gephi/0.8.2/dev/modules/fr-inria-edelweiss-semantic.jar.pack.gz to /home/oracle/.gephi/0.8.2/dev/modules/fr-inria-edelweiss-semantic.jar
INFO [org.netbeans.updater]: File /home/oracle/.gephi/0.8.2/dev/modules/fr-inria-edelweiss-semantic.jar.pack.gz deleted.
INFO [org.netbeans.updater]: File /home/oracle/.gephi/0.8.2/dev/update/download/fr-inria-edelweiss-semantic.nbm deleted.
INFO [org.netbeans.updater]: Use XML Transformer: com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl@6fcbf388
INFO [org.netbeans.updater]: File /home/oracle/.gephi/0.8.2/dev/update_tracking/fr-inria-edelweiss-semantic.xml modified.
INFO [org.netbeans.updater]: File installed /home/oracle/.gephi/0.8.2/dev/update_tracking/fr-inria-edelweiss-semantic.xml@0
INFO [org.netbeans.updater]: File /home/oracle/.gephi/0.8.2/dev/update/download/additional_information.xml deleted.
WARNING [org.netbeans.core.startup.NbEvents]: The extension /home/oracle/.gephi/0.8.2/dev/modules/ext/commons-logging-1.1.1.jar may be multiply loaded by modules: [/home/oracle/.gephi/0.8.2/dev/modules/fr-inria-edelweiss-semantic.jar, /home/oracle/.gephi/0.8.2/dev/modules/net-phreakocious-httpgraph.jar]; see: http://www.netbeans.org/download/dev/ja ... class-path
WARNING [org.netbeans.core.startup.NbEvents]: The extension /home/oracle/.gephi/0.8.2/dev/modules/ext/activation-1.1.jar may be multiply loaded by modules: [/home/oracle/.gephi/0.8.2/dev/modules/fr-inria-edelweiss-semantic.jar, /home/oracle/.gephi/0.8.2/dev/modules/net-phreakocious-httpgraph.jar]; see: http://www.netbeans.org/download/dev/ja ... class-path
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/gephi/gephi/gephi/modules/org-gephi-io-complexgenerator-plugin.jar!/org/gephi/io/complexgenerator/plugin/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/gephi/gephi/gephi/modules/org-gephi-streaming-api.jar!/org/gephi/streaming/api/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/gephi/gephi/gephi/modules/org-gephi-streaming-server.jar!/org/gephi/streaming/server/layer.xml
INFO [org.netbeans.core.startup.NbEvents]: Turning on modules:
fr.inria.edelweiss.semantic/1 [1.20130131 2 130304]
WARNING [org.openide.filesystems.Ordering]: Not all children in Menu/Window/ marked with the position attribute: [fr-inria-edelweiss-SemanticWebImportMainWindowTopComponent.shadow], but some are: [org-gephi-desktop-clustering-ClusteringTopComponent.shadow, org-gephi-desktop-clustering-ContextTopComponent.shadow, org-gephi-desktop-datalab-DataTableTopComponent.shadow, org-gephi-desktop-scripting-ConsoleTopComponent.shadow, org-gephi-desktop-filters-FiltersTopComponent.shadow, org-gephi-visualization-component-GraphTopComponent.shadow, org-gephi-desktop-datalab-HierarchyTopComponent.shadow, org-gephi-desktop-layout-LayoutTopComponent.shadow, org-gephi-desktop-partition-PartitionTopComponent.shadow, org-gephi-desktop-preview-PreviewTopComponent.shadow, org-gephi-desktop-preview-PreviewSettingsTopComponent.shadow, org-gephi-desktop-ranking-RankingTopComponent.shadow, org-gephi-desktop-welcome-WelcomeAction.shadow, org-gephi-desktop-statistics-StatisticsTopComponent.shadow, org-gephi-desktop-timeline-TimelineWindowAction.shadow, org-gephi-desktop-streaming-StreamingTopComponent.shadow, Separator3.instance, ConfigureWindow, Separator4.instance, CloseWindowAction.shadow, Separator4_1.instance]
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: dirURL = file:/home/oracle/.gephi/0.8.2/dev/modules/fr-inria-edelweiss-semantic.jar!/fr/inria/edelweiss/semantic/default_configuration/, protocol = jar
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: META-INF/
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: META-INF/MANIFEST.MF
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: META-INF/services/
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: fr/
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: fr/inria/
...

INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: fr/inria/wimmics/semanticweb/filter/type/TypeFilterBuilder.class
INFO [fr.inria.edelweiss.semantic.configurationmanager.ConfigurationManager]: fr/inria/wimmics/semanticweb/filter/type/TypeFilterPanel.class


-----------

Other than work arounds, what is the solution to get all the updates to work?

Thanks,

R.

[Rodger22]

Here's another update.

Started all over:
cd /home/oracle/.gephi/0.8.2
rm -vrf *


I used the plugin update via the web.
(as opposed to manually downloading and installing them)
Installed plugins one by one.
Rebooted Gephi each time.

When I installed Semantic Web Import, and rebooted, the plugins update window was disabled.

Started again:

cd /home/oracle/.gephi/0.8.2
rm -vrf *

Again, installed plugins one by one.
Rebooted Gephi each time.

All except for Semantic Web Import.
I was able to install everything.
And the Plugin update window was still enabled and working.


Work around for the moment:
Don't install Semantic Web Import