Running ./configure --enable-gnome should work without any issues, though honestly I stopped using WindowMaker a while ago when it hadn't seen any updates for a while, and can't confirm for myself. If you're not generally familiar with installing things from source, you may just want to wait for the repos to be updated. While Fedora's not as bad as some distros, it can take a bit for things to trickle down from upstream. In the long run, it'll probably also be simpler to keep on top of it with yum than building from source if updates become more frequent ago. I'm sure the repos will get updated sooner or later, and then everything ought to be working fine for you.
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