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"Does time spent in the C code show up in the ruby-prof output?"
Yes it does -- There are two stats for method time: "Self" [time in method] - [time spent in called children]), "total" [total time in method]. The second should include time spent in the C code
It was also mentioned that it is much more useful to look at the ruby prof output as HTML or even better using KCachegrind (though it was mentioned that it can be a bit of a pain to get it installed see KCachegrind OS X 10.5.6