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This is most likely a problem with your environment variables. The exact way you need to set the environment variables depends on which distro of ROS you are running (fuerte, groovy, etc.). If you go back to the install instructions for your version, you will notice that there is a step about "sourcing" a setup.bash file. For example in section 1.5 of the fuerte install instructions, you'll a description about how to properly configure your environment. Note that as the link mentions, if you don't add changes to your environment to your .bashrc file, then you will have to change them in every terminal you want to use ROS in.
ROS needs environment variables such as ROS_DISTRO, ROS_MASTER_URI, ROS_PACKAGE_PATH, and more all to be set to function properly. You can check all currently set environment variables with the env command. You can also do something like echo $ROS_DISTRO to see just one environment variable. To see all ROS environment variables you could use env | grep ROS  This is most likely a problem with your environment variables. The exact way you need to set the environment variables depends on which distro of ROS you are running (fuerte, groovy, etc.). If you go back to the install instructions for your version, you will notice that there is a step about "sourcing" a setup.bash file. For example in section 1.5 of the fuerte install instructions, you'll a description about how to properly configure your environment. Note that as the link mentions, if you don't add changes to your environment to your .bashrc file, then you will have to change them in every terminal you want to use ROS in. ROS needs environment variables such as ROS_DISTRO, ROS_MASTER_URI, ROS_PACKAGE_PATH, and more all to be set to function properly. You can check all currently set environment variables with the env command. You can also do something like echo$ROS_DISTRO to see just one environment variable. To see all ROS environment variables you could use
env | grep ROS

Also note that even if your environment variables are all set, they need to be set in agreement with your actual current system setup. For example, if you installed Fuerte following the install instructions, and then switched to Groovy, it's possible your .bashrc file has conflicting commands in it.