Eclipse Timeout Error from the debugger?

I suggest you clean up your eclipse using terminal

Mine directory

cd /Applications/eclipse_juno/Eclipse.app/Contents/MacOS

Clean command

./eclipse -clean

OR

Open up eclipse.ini in your eclipse folder.

Change this line

-Xms512m
-Xmx1024m

into this

-Xms768m
-Xmx768m
eclipse.ini

-startup
../../../plugins/org.eclipse.equinox.launcher_1.3.0.v20120522-1813.jar
--launcher.library
../../../plugins/org.eclipse.equinox.launcher.cocoa.macosx.x86_64_1.1.200.v20120913-144807
-product
org.eclipse.epp.package.jee.product
--launcher.defaultAction
openFile
-showsplash
org.eclipse.platform
--launcher.XXMaxPermSize
256m
--launcher.defaultAction
openFile
-vmargs
-Dosgi.requiredJavaVersion=1.5
-Dhelp.lucene.tokenizer=standard
-XstartOnFirstThread
-Dorg.eclipse.swt.internal.carbon.smallFonts
-XX:MaxPermSize=192m
-Xms768m
-Xmx768m
-Xdock:icon=../Resources/Eclipse.icns
-XstartOnFirstThread
-Dorg.eclipse.swt.internal.carbon.smallFonts

If still happen, restart your machine.

http://blog.revivalx.com/2014/03/15/your-eclipse-always-crash-how-to-fix-and-enhance-to-do-list/

You can increase a value of debugging time out in Eclipse.

Go to Window/Preferences. In the Java/Debug you'll see Debugger Time out parameter.