Develop Reference

Eclipse will not run correctly and stops suddenly

Newly, I've installed an application named Afra (https://rebeca-lang.org/alltools/Afra) which it seems have been developed based on Eclipse. When I'm going to run it won't start and errors below appear in the log file :
(for more information, I use a 64-bit version of windows 10 plus java 10)
!SESSION 2020-09-22 21:29:21.395 -----------------------------------------------
eclipse.buildId=unknown
java.version=10.0.2
java.vendor=Oracle Corporation
BootLoader constants: OS=win32, ARCH=x86_64, WS=win32, NL=en_US
Framework arguments: -clearPersistedState
Command-line arguments: -os win32 -ws win32 -arch x86_64 -clearPersistedState
!ENTRY org.eclipse.osgi 4 0 2020-09-22 21:29:22.797
!MESSAGE Application error
!STACK 1
org.eclipse.e4.core.di.InjectionException: java.lang.NoClassDefFoundError: javax/annotation/PostConstruct
at org.eclipse.e4.core.internal.di.InjectorImpl.internalMake(InjectorImpl.java:410)
at org.eclipse.e4.core.internal.di.InjectorImpl.make(InjectorImpl.java:318)
at org.eclipse.e4.core.contexts.ContextInjectionFactory.make(ContextInjectionFactory.java:162)
at org.eclipse.e4.ui.internal.workbench.swt.E4Application.createDefaultHeadlessContext(E4Application.java:491)
at org.eclipse.e4.ui.internal.workbench.swt.E4Application.createDefaultContext(E4Application.java:505)
at org.eclipse.e4.ui.internal.workbench.swt.E4Application.createE4Workbench(E4Application.java:204)
at org.eclipse.ui.internal.Workbench.lambda$3(Workbench.java:614)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:336)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:594)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:148)
at org.rebecalang.afra.ideplugin.Application.start(Application.java:20)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:653)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
at org.eclipse.equinox.launcher.Main.run(Main.java:1499)
at org.eclipse.equinox.launcher.Main.main(Main.java:1472)
Caused by: java.lang.NoClassDefFoundError: javax/annotation/PostConstruct
at org.eclipse.e4.core.internal.di.InjectorImpl.inject(InjectorImpl.java:124)
at org.eclipse.e4.core.internal.di.InjectorImpl.internalMake(InjectorImpl.java:399)
... 23 more

This looks very much like Afra is based on an older Eclipse platform, and it is caused by using Java 10 instead of Java 8 to run it.
You can do one of the following:
Add Java 8 (64-bit) to the Afra installation, e.g. by download this ZIP file, create the subfolder jre in the Afra installation directory and extract the ZIP into it, so that <Afra-installation-dir>\jre\bin\java.exe exists
Install Java 8 (64-bit) into your system and make sure that Afra runs with it, e.g. by download a Java 8 (64-bit) JDK or JRE from e.g. AdoptOpenJDK.net, install it and in the case it is not used to run Afra, edit the *.ini file of Afra

NetBeans fails to start from either terminal or GUI in Kali Linux

When I installed NetBeans and ran it for the first time, it told me that NetBeans cannot run on the default openJDK on Kali Linux. So I downloaded and installed JDK32bit from Oracle, and since then it has failed to start. However, when I ran it in the terminal I got this stacktrace. So I thought maybe NetBeans 64bit cannot run on 32bit JDK, so I installed 64bit JDK also, but I am still getting the same problems.
java.net.UnknownHostException: localhost.localdomain: localhost.localdomain: System error
at java.net.InetAddress.getLocalHost(InetAddress.java:1505)
at org.netbeans.CLIHandler$2.run(CLIHandler.java:667)
at org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:1443)
at org.netbeans.modules.openide.util.GlobalLookup.execute(GlobalLookup.java:68)
at org.openide.util.lookup.Lookups.executeWith(Lookups.java:303)
at org.openide.util.RequestProcessor$Processor.run(RequestProcessor.java:2058)
Caused by: java.net.UnknownHostException: localhost.localdomain: System error
at java.net.Inet6AddressImpl.lookupAllHostAddr(Native Method)
at java.net.InetAddress$2.lookupAllHostAddr(InetAddress.java:928)
at java.net.InetAddress.getAddressesFromNameService(InetAddress.java:1323)
at java.net.InetAddress.getLocalHost(InetAddress.java:1500)
... 5 more
I just discovered the same applies to Eclipse also, it fails to start and this is the log report:
!SESSION 2017-10-02 23:35:37.652 -----------------------------------------------
eclipse.buildId=4.7.0.I20170612-0950
java.version=1.8.0_144
java.vendor=Oracle Corporation
BootLoader constants: OS=linux, ARCH=x86, WS=gtk, NL=en_NG
Framework arguments: -product org.eclipse.epp.package.jee.product
Command-line arguments: -os linux -ws gtk -arch x86 -product org.eclipse.epp.package.jee.product
!ENTRY org.eclipse.osgi 4 0 2017-10-02 23:35:55.129
!MESSAGE Application error
!STACK 1
java.lang.UnsatisfiedLinkError: Could not load SWT library. Reasons:
/home/MW/eclipse/configuration/org.eclipse.osgi/781/0/.cp/libswt-pi3-gtk-4757.so: libgtk-3.so.0: cannot open shared object file: No such file or directory
no swt-pi3-gtk in java.library.path
/home/MW/.swt/lib/linux/x86/libswt-pi3-gtk-4757.so: libgtk-3.so.0: cannot open shared object file: No such file or directory
Can't load library: /home/MW/.swt/lib/linux/x86/libswt-pi3-gtk.so
at org.eclipse.swt.internal.Library.loadLibrary(Library.java:327)
at org.eclipse.swt.internal.Library.loadLibrary(Library.java:236)
at org.eclipse.swt.internal.gtk.OS.<clinit>(OS.java:58)
at org.eclipse.swt.internal.Converter.wcsToMbcs(Converter.java:124)
at org.eclipse.swt.internal.Converter.wcsToMbcs(Converter.java:80)
at org.eclipse.swt.widgets.Display.<clinit>(Display.java:140)
at org.eclipse.ui.internal.Workbench.createDisplay(Workbench.java:765)
at org.eclipse.ui.PlatformUI.createDisplay(PlatformUI.java:160)
at org.eclipse.ui.internal.ide.application.IDEApplication.createDisplay(IDEApplication.java:181)
at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:124)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:653)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
at org.eclipse.equinox.launcher.Main.run(Main.java:1499)
!ENTRY com.genuitec.eclipse.theming.core 4 0 2017-10-02 23:35:55.414
!MESSAGE <null>
!STACK 0
Unexpected token RIGHT SQUARE(]) at position 0.
at org.json.simple.parser.JSONParser.parse(JSONParser.java:257)
at org.json.simple.parser.JSONParser.parse(JSONParser.java:92)
at com.genuitec.eclipse.theming.core.services.ImageReplacementService.loadUnknownImages(ImageReplacementService.java:91)
at com.genuitec.eclipse.theming.core.services.ImageReplacementService.<init>(ImageReplacementService.java:74)
at com.genuitec.eclipse.theming.core.services.ImageReplacementService.<clinit>(ImageReplacementService.java:38)
at com.genuitec.eclipse.theming.core.ThemingCorePlugin.stop(ThemingCorePlugin.java:77)
at org.eclipse.osgi.internal.framework.BundleContextImpl$4.run(BundleContextImpl.java:835)
at org.eclipse.osgi.internal.framework.BundleContextImpl$4.run(BundleContextImpl.java:1)
at java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.internal.framework.BundleContextImpl.stop(BundleContextImpl.java:828)
at org.eclipse.osgi.internal.framework.EquinoxBundle.stopWorker0(EquinoxBundle.java:947)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.stopWorker(EquinoxBundle.java:314)
at org.eclipse.osgi.container.Module.doStop(Module.java:636)
at org.eclipse.osgi.container.Module.stop(Module.java:498)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.decStartLevel(ModuleContainer.java:1669)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.doContainerStartLevel(ModuleContainer.java:1588)
at org.eclipse.osgi.container.SystemModule.stopWorker(SystemModule.java:270)
at org.eclipse.osgi.internal.framework.EquinoxBundle$SystemBundle$EquinoxSystemModule.stopWorker(EquinoxBundle.java:147)
at org.eclipse.osgi.container.Module.doStop(Module.java:636)
at org.eclipse.osgi.container.Module.stop(Module.java:498)
at org.eclipse.osgi.container.SystemModule.stop(SystemModule.java:202)
at org.eclipse.osgi.internal.framework.EquinoxBundle$SystemBundle$EquinoxSystemModule$1.run(EquinoxBundle.java:165)
at java.lang.Thread.run(Thread.java:748)

JUnit Plug-in Test Ignores Target Platform in Eclipse Neon

I have some problems getting JUnit plug-in tests to work using Eclipse Neon M7 and I'd really like input from anybody out there who uses tests (there has to be somebody, right?).
Whenever I start a test that works in Eclipse Luna (but didn't in Mars, which I assumed was a bug) and continues to work using Tycho I get the following exception:
!SESSION 2016-05-11 10:25:41.456 -----------------------------------------------
eclipse.buildId=unknown
java.version=1.8.0_73
java.vendor=Oracle Corporation
BootLoader constants: OS=win32, ARCH=x86, WS=win32, NL=en_US
Framework arguments: -version 3 -port 60297 -testLoaderClass org.eclipse.jdt.internal.junit4.runner.JUnit4TestLoader -loaderpluginname org.eclipse.jdt.junit4.runtime -classNames org.acme.test.test.core.ActivatorTest -application org.eclipse.pde.junit.runtime.uitestapplication -testApplication org.eclipse.ui.ide.workbench -testpluginname test.core
Command-line arguments: -os win32 -ws win32 -arch x86 -consoleLog -version 3 -port 60297 -testLoaderClass org.eclipse.jdt.internal.junit4.runner.JUnit4TestLoader -loaderpluginname org.eclipse.jdt.junit4.runtime -classNames org.acme.test.test.core.ActivatorTest -application org.eclipse.pde.junit.runtime.uitestapplication -testApplication org.eclipse.ui.ide.workbench -data C:\workspaces\MyWorkspace/../junit-workspace -dev file:C:/workspaces/MyWorkspace/.metadata/.plugins/org.eclipse.pde.core/pde-junit/dev.properties -os win32 -ws win32 -arch x86 -consoleLog -testpluginname test.core
!ENTRY org.eclipse.pde.junit.runtime 4 0 2016-05-11 10:25:42.373
!MESSAGE FrameworkEvent ERROR
!STACK 0
org.osgi.framework.BundleException: Could not resolve module: org.eclipse.pde.junit.runtime [81]
Unresolved requirement: Require-Bundle: org.eclipse.core.runtime; bundle-version="[3.11.0,4.0.0)"
at org.eclipse.osgi.container.Module.start(Module.java:434)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1582)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1561)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.doContainerStartLevel(ModuleContainer.java:1533)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1476)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1)
at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:230)
at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:340)
!ENTRY org.eclipse.pde.junit.runtime 2 0 2016-05-11 10:25:42.719
!MESSAGE Could not resolve module: org.eclipse.pde.junit.runtime [81]
Unresolved requirement: Require-Bundle: org.eclipse.core.runtime; bundle-version="[3.11.0,4.0.0)"
!ENTRY org.eclipse.osgi 4 0 2016-05-11 10:25:42.720
!MESSAGE Application error
!STACK 1
java.lang.RuntimeException: Application "org.eclipse.pde.junit.runtime.uitestapplication" could not be found in the registry. The applications available are: org.eclipse.ant.core.antRunner, org.eclipse.ui.ide.workbench, org.eclipse.help.base.infocenterApplication, org.eclipse.help.base.helpApplication, org.eclipse.help.base.indexTool, org.acme.test.rxp.rxpdemo, org.eclipse.equinox.app.error.
at org.eclipse.equinox.internal.app.EclipseAppContainer.startDefaultApp(EclipseAppContainer.java:248)
at org.eclipse.equinox.internal.app.MainApplicationLauncher.run(MainApplicationLauncher.java:29)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:382)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:236)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
at org.eclipse.equinox.launcher.Main.main(Main.java:1386)
Clearly it's not a Eclipse bug at this point, but I'm doing something wrong. There is no indication what kind of plug-ins are started in the test, but judging from the version ranges I assume it's the wrong ones again - the plug-ins of the running Eclipse instance instead of the plug-ins defined in the workspace's target platform.
Still the launch configuration claims the later target platform is used.
How do I configure a plug-in unit test so that it will take the currently active target platform?

The problem here is that Eclipse 4.4 (Luna, 2014) and below had a version of org.eclipse.core.runtime that was compatible with the host Eclipse version of org.eclipse.pde.junit.runtime. That changed with 4.5 when the dependency increased.
As you have correctly concluded that the configuration is pointing at the wrong org.eclipse.pde.junit.runtime. This is probably due to uncleared configuration state. Ensure that the configuration is being cleared, so you don't run with a stale version. That is ensure that Clear the configuration area before launching is checked in the Configuration tab of launch configuration.
You can see exactly what PDE has resolved as the configured bundles by looking at ${workspace_loc}/.metadata/.plugins/org.eclipse.pde.core/pde-junit/org.eclipse.equinox.simpleconfigurator/bundles.info (location specified in Configuration tab of launch configuration)

java eclipse fail to load

Ive just installed eclipse and when i try to open it it fails.
Would really appreciate it if anyone could help me with whats gone wrong/ how to fix it.
this is the log:
!SESSION 2013-01-17 16:18:49.511 -----------------------------------------------
eclipse.buildId=I20110613-1736
java.version=1.7.0_11
java.vendor=Oracle Corporation
BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_NZ
Command-line arguments: -os linux -ws gtk -arch x86_64
!ENTRY org.eclipse.osgi 4 0 2013-01-17 16:18:50.613
!MESSAGE Application error
!STACK 1
java.lang.UnsatisfiedLinkError: Could not load SWT library. Reasons:
no swt-gtk-3740 in java.library.path
no swt-gtk in java.library.path
Can't load library: /home/calum/.swt/lib/linux/x86_64/libswt-gtk-3740.so
Can't load library: /home/calum/.swt/lib/linux/x86_64/libswt-gtk.so
at org.eclipse.swt.internal.Library.loadLibrary(Library.java:285)
at org.eclipse.swt.internal.Library.loadLibrary(Library.java:194)
at org.eclipse.swt.internal.C.<clinit>(C.java:21)
at org.eclipse.swt.internal.Converter.wcsToMbcs(Converter.java:63)
at org.eclipse.swt.internal.Converter.wcsToMbcs(Converter.java:54)
at org.eclipse.swt.widgets.Display.<clinit>(Display.java:132)
at org.eclipse.ui.internal.Workbench.createDisplay(Workbench.java:695)
at org.eclipse.ui.PlatformUI.createDisplay(PlatformUI.java:161)
at org.eclipse.ui.internal.ide.application.IDEApplication.createDisplay(IDEApplication.java:153)
at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:95)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:>79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
at org.eclipse.equinox.launcher.Main.main(Main.java:1386)

Try these steps.
If you are using debian based os, use
sudo apt-get install eclipse-platform
It's maintained. Else download the IDE for linux from here.
Install OpenJDK not oracle java 7.
sudo apt-get install openjdk-7-jdk
If you need to use oracle jdk, see this article. It's working for me in Ubuntu 12.10

Try this:
ln -s /usr/lib/jni/libswt-* ~/.swt/lib/linux/x86_64/

Can't start Eclipse

I can't start eclipse 3.6 helios on ubuntu 10.10 after creating dynamic web project running on internal glassfish server.
I can switch workspace and then eclipse starts.
Using workspace with created Java EE project # GlassFish prevents eclipse to start.
Deleting .metadata/.lock and .metadata/.log doesn't help.
I have stopped all my containers (Tomcat, GlassFish, Jetty).
Restarting PC doesn't help.
Here's what I found in .log file:
!SESSION 2011-03-13 13:47:10.068 -----------------------------------------------
eclipse.buildId=M20110210-1200
java.version=1.6.0_24
java.vendor=Sun Microsystems Inc.
BootLoader constants: OS=linux, ARCH=x86, WS=gtk, NL=en_US
Framework arguments: -product org.eclipse.epp.package.jee.product
Command-line arguments: -os linux -ws gtk -arch x86 -product org.eclipse.epp.package.jee.product
!ENTRY oracle.eclipse.tools.glassfish 4 1 2011-03-13 13:47:15.258
!MESSAGE GlassFish: Already Registered: /home/miso/eclipse/plugins/oracle.eclipse.runtime.glassfish_3.1.0.0/glassfish3/glassfish
!ENTRY com.google.gwt.eclipse.core 4 0 2011-03-13 13:47:16.439
!MESSAGE Could not start source viewer server.
!STACK 0
java.net.BindException: Address already in use
at java.net.PlainSocketImpl.socketBind(Native Method)
at java.net.PlainSocketImpl.bind(PlainSocketImpl.java:383)
at java.net.ServerSocket.bind(ServerSocket.java:328)
at java.net.ServerSocket.<init>(ServerSocket.java:194)
at java.net.ServerSocket.<init>(ServerSocket.java:150)
at org.mortbay.jetty.bio.SocketConnector.newServerSocket(SocketConnector.java:80)
at org.mortbay.jetty.bio.SocketConnector.open(SocketConnector.java:73)
at org.mortbay.jetty.AbstractConnector.doStart(AbstractConnector.java:283)
at org.mortbay.jetty.bio.SocketConnector.doStart(SocketConnector.java:147)
at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
at org.mortbay.jetty.Server.doStart(Server.java:235)
at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
at com.google.gdt.eclipse.platform.jetty.JettyServer.start(JettyServer.java:62)
at com.google.gwt.eclipse.core.GWTPlugin.start(GWTPlugin.java:116)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl$1.run(BundleContextImpl.java:783)
at java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.startActivator(BundleContextImpl.java:774)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.start(BundleContextImpl.java:755)
at org.eclipse.osgi.framework.internal.core.BundleHost.startWorker(BundleHost.java:370)
at org.eclipse.osgi.framework.internal.core.AbstractBundle.start(AbstractBundle.java:284)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:417)
at org.eclipse.osgi.internal.loader.BundleLoader.setLazyTrigger(BundleLoader.java:265)
at org.eclipse.core.runtime.internal.adaptor.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:106)
at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClass(ClasspathManager.java:453)
at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.findLocalClass(DefaultClassLoader.java:216)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:393)
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:469)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:422)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:410)
at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass(DefaultClassLoader.java:107)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
at org.eclipse.osgi.internal.loader.BundleLoader.loadClass(BundleLoader.java:338)
at org.eclipse.osgi.framework.internal.core.BundleHost.loadClass(BundleHost.java:232)
at org.eclipse.osgi.framework.internal.core.AbstractBundle.loadClass(AbstractBundle.java:1197)
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:174)
at org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension(ExtensionRegistry.java:904)
at org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension(ConfigurationElement.java:243)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension(ConfigurationElementHandle.java:55)
at org.eclipse.core.internal.content.ContentType.getDescriber(ContentType.java:271)
at org.eclipse.core.internal.content.ContentTypeCatalog.collectMatchingByContents(ContentTypeCatalog.java:184)
at org.eclipse.core.internal.content.ContentTypeCatalog.internalFindContentTypesFor(ContentTypeCatalog.java:401)
at org.eclipse.core.internal.content.ContentTypeCatalog.internalFindContentTypesFor(ContentTypeCatalog.java:450)
at org.eclipse.core.internal.content.ContentTypeCatalog.getDescriptionFor(ContentTypeCatalog.java:346)
at org.eclipse.core.internal.content.ContentTypeCatalog.getDescriptionFor(ContentTypeCatalog.java:360)
at org.eclipse.core.internal.content.ContentTypeMatcher.getDescriptionFor(ContentTypeMatcher.java:86)
at org.eclipse.core.internal.resources.ContentDescriptionManager.readDescription(ContentDescriptionManager.java:436)
at org.eclipse.core.internal.resources.ContentDescriptionManager.getDescriptionFor(ContentDescriptionManager.java:346)
at org.eclipse.core.internal.resources.File.getContentDescription(File.java:275)
at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl.createResource(ProjectResourceSetImpl.java:728)
at org.eclipse.wst.common.internal.emfworkbench.integration.ProjectResourceSetEditImpl.createResource(ProjectResourceSetEditImpl.java:49)
at org.eclipse.emf.ecore.resource.impl.ResourceSetImpl.demandCreateResource(ResourceSetImpl.java:239)
at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl.getResource(ProjectResourceSetImpl.java:1057)
at org.eclipse.wst.common.internal.emfworkbench.WorkbenchResourceHelper.getOrCreateResource(WorkbenchResourceHelper.java:380)
at org.eclipse.wst.common.internal.emfworkbench.integration.EditModel.getResource(EditModel.java:685)
at org.eclipse.wst.common.componentcore.internal.ModuleStructuralModel.getPrimaryResource(ModuleStructuralModel.java:332)
at org.eclipse.wst.common.componentcore.internal.ModuleStructuralModel.prepareProjectModulesIfNecessary(ModuleStructuralModel.java:240)
at org.eclipse.wst.common.componentcore.internal.ModuleStructuralModel.getPrimaryRootObject(ModuleStructuralModel.java:119)
at org.eclipse.wst.common.componentcore.internal.StructureEdit.getComponentModelRoot(StructureEdit.java:436)
at org.eclipse.wst.common.componentcore.internal.StructureEdit.getWorkbenchModules(StructureEdit.java:471)
at org.eclipse.wst.common.componentcore.internal.StructureEdit.getComponent(StructureEdit.java:914)
at org.eclipse.wst.common.componentcore.internal.resources.VirtualComponent.createResource(VirtualComponent.java:122)
at org.eclipse.wst.common.componentcore.internal.resources.VirtualComponent.initializeResource(VirtualComponent.java:111)
at org.eclipse.wst.common.componentcore.internal.resources.VirtualComponent.<init>(VirtualComponent.java:146)
at org.eclipse.jst.j2ee.componentcore.J2EEModuleVirtualComponent.<init>(J2EEModuleVirtualComponent.java:88)
at org.eclipse.jst.j2ee.componentcore.J2EEModuleVirtualComponent.createComponent(J2EEModuleVirtualComponent.java:92)
at org.eclipse.wst.common.componentcore.internal.util.ComponentImplManager.createComponent(ComponentImplManager.java:215)
at org.eclipse.wst.common.componentcore.internal.util.ComponentImplManager.createComponent(ComponentImplManager.java:203)
at org.eclipse.wst.common.componentcore.ComponentCore.createComponent(ComponentCore.java:64)
at org.eclipse.jst.j2ee.internal.deployables.J2EEDeployableFactory.createModules(J2EEDeployableFactory.java:87)
at org.eclipse.wst.server.core.util.ProjectModuleFactoryDelegate.cacheModules(ProjectModuleFactoryDelegate.java:60)
at org.eclipse.wst.server.core.util.ProjectModuleFactoryDelegate.findModule(ProjectModuleFactoryDelegate.java:270)
at org.eclipse.wst.server.core.internal.ModuleFactory.findModule(ModuleFactory.java:197)
at org.eclipse.wst.server.core.ServerUtil.getModule(ServerUtil.java:136)
at org.eclipse.wst.server.core.internal.Server.getModules(Server.java:2314)
at org.eclipse.wst.server.ui.internal.cnf.ServerContentProvider.hasChildren(ServerContentProvider.java:96)
at org.eclipse.ui.internal.navigator.extensions.SafeDelegateTreeContentProvider.hasChildren(SafeDelegateTreeContentProvider.java:110)
at org.eclipse.ui.internal.navigator.NavigatorContentServiceContentProvider.callNormalHasChildren(NavigatorContentServiceContentProvider.java:428)
at org.eclipse.ui.internal.navigator.NavigatorContentServiceContentProvider.access$4(NavigatorContentServiceContentProvider.java:423)
at org.eclipse.ui.internal.navigator.NavigatorContentServiceContentProvider$3.run(NavigatorContentServiceContentProvider.java:393)
at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
at org.eclipse.ui.internal.navigator.NavigatorContentServiceContentProvider.hasChildren(NavigatorContentServiceContentProvider.java:379)
at org.eclipse.ui.internal.navigator.NavigatorContentServiceContentProvider.hasChildren(NavigatorContentServiceContentProvider.java:420)
at org.eclipse.jface.viewers.AbstractTreeViewer.isExpandable(AbstractTreeViewer.java:2082)
at org.eclipse.jface.viewers.TreeViewer.isExpandable(TreeViewer.java:588)
at org.eclipse.jface.viewers.AbstractTreeViewer.isExpandable(AbstractTreeViewer.java:2112)
at org.eclipse.jface.viewers.AbstractTreeViewer.updatePlus(AbstractTreeViewer.java:2794)
at org.eclipse.jface.viewers.TreeViewer.updatePlus(TreeViewer.java:852)
at org.eclipse.jface.viewers.AbstractTreeViewer.createTreeItem(AbstractTreeViewer.java:830)
at org.eclipse.jface.viewers.AbstractTreeViewer$1.run(AbstractTreeViewer.java:804)
at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
at org.eclipse.jface.viewers.AbstractTreeViewer.createChildren(AbstractTreeViewer.java:778)
at org.eclipse.jface.viewers.TreeViewer.createChildren(TreeViewer.java:644)
at org.eclipse.jface.viewers.AbstractTreeViewer.createChildren(AbstractTreeViewer.java:749)
at org.eclipse.jface.viewers.AbstractTreeViewer.internalInitializeTree(AbstractTreeViewer.java:1492)
at org.eclipse.jface.viewers.TreeViewer.internalInitializeTree(TreeViewer.java:833)
at org.eclipse.jface.viewers.AbstractTreeViewer$5.run(AbstractTreeViewer.java:1476)
at org.eclipse.jface.viewers.StructuredViewer.preservingSelection(StructuredViewer.java:1422)
at org.eclipse.jface.viewers.TreeViewer.preservingSelection(TreeViewer.java:403)
at org.eclipse.jface.viewers.StructuredViewer.preservingSelection(StructuredViewer.java:1383)
at org.eclipse.jface.viewers.AbstractTreeViewer.inputChanged(AbstractTreeViewer.java:1469)
at org.eclipse.jface.viewers.ContentViewer.setInput(ContentViewer.java:274)
at org.eclipse.jface.viewers.StructuredViewer.setInput(StructuredViewer.java:1664)
at org.eclipse.ui.navigator.CommonNavigator.createPartControl(CommonNavigator.java:212)
at org.eclipse.wst.server.ui.internal.cnf.ServersView2.createPartControl(ServersView2.java:63)
at org.eclipse.ui.internal.ViewReference.createPartHelper(ViewReference.java:375)
at org.eclipse.ui.internal.ViewReference.createPart(ViewReference.java:229)
at org.eclipse.ui.internal.WorkbenchPartReference.getPart(WorkbenchPartReference.java:595)
at org.eclipse.ui.internal.WorkbenchPage$ActivationList.setActive(WorkbenchPage.java:4218)
at org.eclipse.ui.internal.WorkbenchPage$18.runWithException(WorkbenchPage.java:3277)
at org.eclipse.ui.internal.StartupThreading$StartupRunnable.run(StartupThreading.java:31)
at org.eclipse.swt.widgets.RunnableLock.run(RunnableLock.java:35)
at org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Synchronizer.java:134)
at org.eclipse.swt.widgets.Display.runAsyncMessages(Display.java:3515)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3164)
at org.eclipse.ui.application.WorkbenchAdvisor.openWindows(WorkbenchAdvisor.java:803)
at org.eclipse.ui.internal.Workbench$31.runWithException(Workbench.java:1567)
at org.eclipse.ui.internal.StartupThreading$StartupRunnable.run(StartupThreading.java:31)
at org.eclipse.swt.widgets.RunnableLock.run(RunnableLock.java:35)
at org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Synchronizer.java:134)
at org.eclipse.swt.widgets.Display.runAsyncMessages(Display.java:3515)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3164)
at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2548)
at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2438)
at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:671)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:664)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:115)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:369)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:620)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:575)
at org.eclipse.equinox.launcher.Main.run(Main.java:1408)

I would nuke your .project file and all associated metadata, uninstall the glassfish plugin, attempt re-import of the project and reinstall the plugin.
You may also consider just running glassfish outside of eclipse and deploying the build binaries with an Ant Script/Maven. I have had nothing but trouble with those eclipse server adapters