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I had the same problem, changing my launcher to source setup.bash solved it.

Create a file called "Eclipse.desktop" and paste the below text into it, possibly replacing /opt/eclipse with wherever your Eclipse installation is located.

#!/usr/bin/env xdg-open

[Desktop Entry]
Version=1.0
Type=Application
Terminal=false
Icon[en_US]=/opt/eclipse/icon.xpm
Exec=bash -c "source /opt/ros/fuerte/setup.bash; /opt/eclipse/eclipse"
Name[en_US]=Eclipse
Name=Eclipse
Icon=/opt/eclipse/icon.xpm

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