freebsd-ports/cad/linux-eagle5/pkg-message

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Eagle needs to be run as "root" first, in order to have write access
to %%PREFIX%%/share/eagle to write a program key file.
Once this has been done, you can delete the "eagle" directory in your
/root directory, which is created during the initially startup, and
run it as a normal user.
It is entirely possible that you need linux 2.6 emulation support
in the kernel. The /usr/ports/UPDATING entry on 20080318 has
good instructions on how to run linux 2.6.16 kernel emulation.