Getting Invalid Registry Object while uninstalling plugins programatically

When a specific condition is hit (while the user is trying to open our perspective), we uninstall the plugins using the below code:
Platform.getBundle(<Bundle name>).uninstall();
When we run this code on Juno 4.2.2, we are hitting the below exception. This same code was working well in Indigo and other earlier releases. Is there a possible step we need to perform before the uninstall? Any help soon will be appreciated.
org.eclipse.core.runtime.InvalidRegistryObjectException: Invalid registry object
at org.eclipse.core.internal.registry.RegistryObjectManager.basicGetObject(RegistryObjectManager.java:273)
at org.eclipse.core.internal.registry.RegistryObjectManager.getObject(RegistryObjectManager.java:263)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.getConfigurationElement(ConfigurationElementHandle.java:26)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.getParent(ConfigurationElementHandle.java:103)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.getDeclaringExtension(ConfigurationElementHandle.java:93)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.getNamespaceIdentifier(ConfigurationElementHandle.java:130)
at org.eclipse.ui.internal.registry.PerspectiveDescriptor.getPluginId(PerspectiveDescriptor.java:153)
at org.eclipse.ui.activities.WorkbenchActivityHelper.createUnifiedId(WorkbenchActivityHelper.java:180)
at org.eclipse.ui.activities.WorkbenchActivityHelper.getIdentifier(WorkbenchActivityHelper.java:57)
at org.eclipse.ui.activities.WorkbenchActivityHelper.allowUseOf(WorkbenchActivityHelper.java:104)
at org.eclipse.ui.activities.WorkbenchActivityHelper.restrictUseOf(WorkbenchActivityHelper.java:122)
at org.eclipse.ui.internal.registry.PerspectiveRegistry.findPerspectiveWithId(PerspectiveRegistry.java:162)
at org.eclipse.ui.internal.registry.PerspectiveRegistry.findPerspectiveWithId(PerspectiveRegistry.java:156)
at org.eclipse.ui.internal.WorkbenchPage.getPerspectiveDesc(WorkbenchPage.java:2385)
at org.eclipse.ui.internal.WorkbenchPage.getPerspective(WorkbenchPage.java:2375)
at org.eclipse.ui.internal.services.WorkbenchSourceProvider.updateActiveShell(WorkbenchSourceProvider.java:952)
at org.eclipse.ui.internal.services.WorkbenchSourceProvider.getCurrentState(WorkbenchSourceProvider.java:133)
at org.eclipse.ui.internal.services.WorkbenchSourceProvider$6.handleEvent(WorkbenchSourceProvider.java:684)
...

Thanks Thorsten for your hint. We tried closing the perspective and it works half way. We did the following to close the perspective before uninstalling the plugins
IWorkbenchWindow w = PlatformUI.getWorkbench().getActiveWorkbenchWindow();
if (w != null) {
IWorkbenchPage wp = w.getActivePage();
if (wp != null) {
IPerspectiveDescriptor[] p = wp.getOpenPerspectives();
if (p != null && p.length > 1) {
wp.closePerspective(p[p.length - 1], true, true);
After this change, we get back to the perspective we were in before we tried to change perspective and plugins got uninstalled. However when i try to bring up the perspective window again to check if the uninstalled perspective is not visible, i hit the Invalid Registry error again. Below is the trace.
org.eclipse.e4.core.di.InjectionException: org.eclipse.core.runtime.InvalidRegistryObjectException: Invalid registry object
at org.eclipse.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:63)
at org.eclipse.e4.core.internal.di.InjectorImpl.invokeUsingClass(InjectorImpl.java:231)
at org.eclipse.e4.core.internal.di.InjectorImpl.invoke(InjectorImpl.java:212)
at org.eclipse.e4.core.contexts.ContextInjectionFactory.invoke(ContextInjectionFactory.java:131)
at org.eclipse.e4.core.commands.internal.HandlerServiceImpl.executeHandler(HandlerServiceImpl.java:171)
at org.eclipse.e4.core.commands.internal.HandlerServiceImpl.executeHandler(HandlerServiceImpl.java:145)
at org.eclipse.e4.ui.workbench.addons.perspectiveswitcher.PerspectiveSwitcher.selectPerspective(PerspectiveSwitcher.java:476)
at org.eclipse.e4.ui.workbench.addons.perspectiveswitcher.PerspectiveSwitcher.access$6(PerspectiveSwitcher.java:472)
at org.eclipse.e4.ui.workbench.addons.perspectiveswitcher.PerspectiveSwitcher$11.widgetSelected(PerspectiveSwitcher.java:368)
at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:248)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1053)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4169)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3758)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$9.run(PartRenderingEngine.java:1053)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:942)
at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:86)
at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:588)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:543)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
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:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:353)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:180)
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:629)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:584)
at org.eclipse.equinox.launcher.Main.run(Main.java:1438)
at org.eclipse.equinox.launcher.Main.main(Main.java:1414)
Caused by: org.eclipse.core.runtime.InvalidRegistryObjectException: Invalid registry object
at org.eclipse.core.internal.registry.RegistryObjectManager.basicGetObject(RegistryObjectManager.java:273)
at org.eclipse.core.internal.registry.RegistryObjectManager.getObject(RegistryObjectManager.java:263)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.getConfigurationElement(ConfigurationElementHandle.java:26)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.getParent(ConfigurationElementHandle.java:103)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.getDeclaringExtension(ConfigurationElementHandle.java:93)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.getNamespaceIdentifier(ConfigurationElementHandle.java:130)
at org.eclipse.ui.internal.registry.PerspectiveDescriptor.getPluginId(PerspectiveDescriptor.java:153)
at org.eclipse.ui.activities.WorkbenchActivityHelper.createUnifiedId(WorkbenchActivityHelper.java:180)
at org.eclipse.ui.activities.WorkbenchActivityHelper.getIdentifier(WorkbenchActivityHelper.java:57)
at org.eclipse.ui.activities.WorkbenchActivityHelper.allowUseOf(WorkbenchActivityHelper.java:104)
at org.eclipse.ui.activities.WorkbenchActivityHelper.restrictUseOf(WorkbenchActivityHelper.java:122)
at org.eclipse.ui.activities.WorkbenchActivityHelper.restrictCollection(WorkbenchActivityHelper.java:600)
at org.eclipse.ui.internal.registry.PerspectiveRegistry.getPerspectives(PerspectiveRegistry.java:211)
at org.eclipse.ui.internal.dialogs.PerspContentProvider.getElements(PerspContentProvider.java:42)
at org.eclipse.jface.viewers.StructuredViewer.getRawChildren(StructuredViewer.java:1010)
at org.eclipse.jface.viewers.ColumnViewer.getRawChildren(ColumnViewer.java:703)
at org.eclipse.jface.viewers.AbstractTableViewer.getRawChildren(AbstractTableViewer.java:1087)
at org.eclipse.jface.viewers.StructuredViewer.getFilteredChildren(StructuredViewer.java:917)
at org.eclipse.jface.viewers.StructuredViewer.getSortedChildren(StructuredViewer.java:1067)
at org.eclipse.jface.viewers.AbstractTableViewer.internalRefreshAll(AbstractTableViewer.java:701)
at org.eclipse.jface.viewers.AbstractTableViewer.internalRefresh(AbstractTableViewer.java:649)
at org.eclipse.jface.viewers.AbstractTableViewer.internalRefresh(AbstractTableViewer.java:636)
at org.eclipse.jface.viewers.AbstractTableViewer$2.run(AbstractTableViewer.java:592)
at org.eclipse.jface.viewers.StructuredViewer.preservingSelection(StructuredViewer.java:1443)
at org.eclipse.jface.viewers.StructuredViewer.preservingSelection(StructuredViewer.java:1404)
at org.eclipse.jface.viewers.AbstractTableViewer.inputChanged(AbstractTableViewer.java:590)
at org.eclipse.jface.viewers.ContentViewer.setInput(ContentViewer.java:280)
at org.eclipse.jface.viewers.StructuredViewer.setInput(StructuredViewer.java:1690)
at org.eclipse.ui.internal.dialogs.SelectPerspectiveDialog.createViewer(SelectPerspectiveDialog.java:198)
at org.eclipse.ui.internal.dialogs.SelectPerspectiveDialog.createDialogArea(SelectPerspectiveDialog.java:134)
at org.eclipse.jface.dialogs.Dialog.createContents(Dialog.java:760)
at org.eclipse.jface.window.Window.create(Window.java:431)
at org.eclipse.jface.dialogs.Dialog.create(Dialog.java:1089)
at org.eclipse.jface.window.Window.open(Window.java:790)
at org.eclipse.ui.handlers.ShowPerspectiveHandler.openOther(ShowPerspectiveHandler.java:101)
at org.eclipse.ui.handlers.ShowPerspectiveHandler.execute(ShowPerspectiveHandler.java:57)
at org.eclipse.ui.internal.handlers.HandlerProxy.execute(HandlerProxy.java:290)
at org.eclipse.ui.internal.handlers.E4HandlerProxy.execute(E4HandlerProxy.java:76)
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.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:56)
... 35 more
I get the following exception when i try to click the finish button to create a new java project.
org.eclipse.core.runtime.InvalidRegistryObjectException: Invalid registry object
at org.eclipse.core.internal.registry.RegistryObjectManager.basicGetObject(RegistryObjectManager.java:273)
at org.eclipse.core.internal.registry.RegistryObjectManager.getObject(RegistryObjectManager.java:263)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.getConfigurationElement(ConfigurationElementHandle.java:26)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.getParent(ConfigurationElementHandle.java:103)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.getDeclaringExtension(ConfigurationElementHandle.java:93)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.getNamespaceIdentifier(ConfigurationElementHandle.java:130)
at org.eclipse.ui.internal.registry.PerspectiveDescriptor.getPluginId(PerspectiveDescriptor.java:153)
at org.eclipse.ui.activities.WorkbenchActivityHelper.createUnifiedId(WorkbenchActivityHelper.java:180)
at org.eclipse.ui.activities.WorkbenchActivityHelper.getIdentifier(WorkbenchActivityHelper.java:57)
at org.eclipse.ui.activities.WorkbenchActivityHelper.allowUseOf(WorkbenchActivityHelper.java:104)
at org.eclipse.ui.activities.WorkbenchActivityHelper.restrictUseOf(WorkbenchActivityHelper.java:122)
at org.eclipse.ui.activities.WorkbenchActivityHelper.restrictCollection(WorkbenchActivityHelper.java:600)
at org.eclipse.ui.internal.registry.PerspectiveRegistry.getPerspectives(PerspectiveRegistry.java:211)
at org.eclipse.ui.wizards.newresource.BasicNewProjectResourceWizard.addPerspectiveAndDescendants(BasicNewProjectResourceWizard.java:545)
at org.eclipse.ui.wizards.newresource.BasicNewProjectResourceWizard.updatePerspective(BasicNewProjectResourceWizard.java:487)
at org.eclipse.jdt.internal.ui.wizards.JavaProjectWizard.performFinish(JavaProjectWizard.java:99)
at org.eclipse.jface.wizard.WizardDialog.finishPressed(WizardDialog.java:827)
at org.eclipse.jface.wizard.WizardDialog.buttonPressed(WizardDialog.java:432)
at org.eclipse.jface.dialogs.Dialog$2.widgetSelected(Dialog.java:624)
at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:248)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1053)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4169)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3758)
at org.eclipse.jface.window.Window.runEventLoop(Window.java:825)
at org.eclipse.jface.window.Window.open(Window.java:801)
at org.eclipse.ui.internal.actions.NewWizardShortcutAction.run(NewWizardShortcutAction.java:135)
at org.eclipse.jface.action.Action.runWithEvent(Action.java:498)
at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:584)
at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:501)
at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:411)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1053)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4169)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3758)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$9.run(PartRenderingEngine.java:1053)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:942)
at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:86)
at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:588)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:543)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
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:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:353)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:180)
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:629)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:584)
at org.eclipse.equinox.launcher.Main.run(Main.java:1438)
at org.eclipse.equinox.launcher.Main.main(Main.java:1414)

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