EMBOSS included non-free files. See debian bug number "694908" datails.
I think that this package be affected by debian bug number "694908".
1. Remove non-free code, and rebuild.
2. Replace fedora free (Fedora acceptable licensed) files.
3. Remove fedora repos.
Blocking FE-Legal, This is license problem.
Did you read Debian Bug 694908? :)
Debian did the hard work of confirming the licensing of the EMBOSS included ontologies. The only necessary change to EMBOSS is to update the license tag in the Fedora package to reflect that.
I've made those changes in EMBOSS-6.4.0-11.fc21 (and f20, since it is not yet released).