I had the same error message in Eclipse 3.4.1, SUN JVM1.6.0_07 connected to Tomcat 6.0 (running in debug-mode on a different machine, Sun JVM1.6.0_16, the debug connection did work correctly).
Window --> Preferences --> Java --> Compiler --> Classfile Generation: "add line number attributes to generated class file" was checked. I did a clean, recompile. I did uncheck it, recompile, check it, recompile. I made sure the project did use the global settings. Still the same message.
I switched to ant build, using
<javac srcdir="./src/java" destdir="./bin" debug="true">
Still, same message.
I didn't find out what caused this message and why it wouldn't go away. Though it seemed to have something to do with the running Tomcat debug session: when disconnected, recompiling solves the issue. But on connecting the debugger to Tomcat or on setting new breakpoints during a connected debug session, it appeared again.
However, it turned out the message was wrong: I was indeed able to debug and set breakpoints, both before and during debugging (javap -l did show line numbers, too). So just ignore it :)
Answer from Zefiro on Stack OverflowI had the same error message in Eclipse 3.4.1, SUN JVM1.6.0_07 connected to Tomcat 6.0 (running in debug-mode on a different machine, Sun JVM1.6.0_16, the debug connection did work correctly).
Window --> Preferences --> Java --> Compiler --> Classfile Generation: "add line number attributes to generated class file" was checked. I did a clean, recompile. I did uncheck it, recompile, check it, recompile. I made sure the project did use the global settings. Still the same message.
I switched to ant build, using
<javac srcdir="./src/java" destdir="./bin" debug="true">
Still, same message.
I didn't find out what caused this message and why it wouldn't go away. Though it seemed to have something to do with the running Tomcat debug session: when disconnected, recompiling solves the issue. But on connecting the debugger to Tomcat or on setting new breakpoints during a connected debug session, it appeared again.
However, it turned out the message was wrong: I was indeed able to debug and set breakpoints, both before and during debugging (javap -l did show line numbers, too). So just ignore it :)
- In eclipse menu, go to Window->Preferences->Java->Compiler
- Unmark checkbox "Add line number attributes..."
- Click Apply -> Yes
- Mark checkbox "Add line number attribute..."
- Apply again.
- Go happy debugging
Unable to install breakpoint due to missing line numbers - Genuitec
java - Eclipse Unable to install breakpoint - Stack Overflow
Unable to install breakpoint in Eclipse: Absent Line Number Information
why can't I set up a breakpoint in eclipse? - Stack Overflow
In order to re enable the message : Preferences => java => debug . it is at the bottom of the screen : "Warn when unable to install breakpoint du to missing line number attributes"
For the problem about installing breakpoints, try to add a -g to your javac command line in ant (debug attribute of you compilation task, http://ant.apache.org/manual/Tasks/javac.html)
Eventually check if you have not mapped your project on a JRE instead of a JDK in eclipse.
This error might also be generated if your Eclipse workspace simply has some invalid (stale or corrupted) breakpoints set. In the Breakpoints view, look for breakpoints that might be set in classes that were moved or deleted, and delete them.
You've probably just pressed "Skip All Breakpoints" in the Breakpoint view - simply press it again.

Default key bindings are: Ctrl + Alt + B.
This doesn't exactly answer the OPs question, but when trying to double click to add break points, I was getting messages stating "this feature is not enabled".
I had to right click on the break point bar and select "Breakpoint Types" -> "C/C++ Breakpoints" instead of "Default". Then it worked fine.
I have had the same problem, but reading your post helped me resolve mine. I changed org.eclipse.jdt.core.prefs as follow:
BEFORE:
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
org.eclipse.jdt.core.compiler.compliance=1.7
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.source=1.7
AFTER:
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
org.eclipse.jdt.core.compiler.compliance=1.7
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.source=1.7
Another way to modify these options within the Project> Properties> Java Compiler. So, there is no need to modify manually the org.eclipse.jdt.core.prefs file. There you need to make sure that the Classfile Generation options are checked.
In the JAR the line number attributes are missing in the compiled bytecode. With the added source code Eclipse knows the line numbers, but not the Java VM that executes the bytecode and does not see the source code.
It would be useless if Eclipse told the Java VM to stop at a specific line, because the Java VM does not know which command is in which line and so when to stop.
The only solution is to recreate the JAR or at least the bytecode (.class files) with line information of the class(es) where you want to set a breakpoint.
One probable issue could come from your application server in IDE pointing to JRE instead of JDK.
Try verifying:
Window -> Preferences --> Server --> runtime environments
<Your-Application-Server> --> edit
Select a JDK instead of JRE
Not sure if you have gone through this link.... has few solutions which worked for some.
Eclipse - Unable to install breakpoint due to missing line number attributes
this happens when you use JRE on your build path in this case.
Try do this:
Window -> Preferences --> Java --> Installed JRES-->then use jdk as default JRE
problem fixed!
I had the same issue and couldnt find a solution.
I eventualy selected "Restore Defaults" button and selected "apply" button and my problem was solved.
Are you trying to set a breakpoint in the source file? Or did you open the Class file and trying to set the breakpoint? If the source file is in a different project and if you have added the compiled jar of that project in another project, you might get this error.