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The issue was fixed. the reason for the error is, I opened the entire build directory in eclipse instead of just one package.

Now i am building only one package from terminal using 'cmake -G"Eclipse CDT4 - Unix Makefiles' . This command needs to run from inside the package directory. After that, i am importing the same package from the eclipse.

In order to build package from eclipse, first i need to compile the code using roamake command from the terminal (inside the package directory), and specified the generated binary files location in eclipse runtime configurations.

After following above steps, all errors gone, and i was able to run the ros packages from eclipse.