Hi Yasmin,
When upgrading from Mavericks to Yosemite, you shouldn't need to recompile packages built from source (although it would still be prudent to).
The biggest OS X change was with the switch from Snow Leopard to Mavericks -- with that change, the default compiler on OS X changed from 'gcc' to 'clang', and this caused a large number of headaches everywhere (since things built with 'gcc' did not work with things built with 'clang').
Since both Mavericks and Yosemite both provide and use 'clang' by default, you shouldn't see any of the same issues as before.
That said, I agree that packrat should be doing some more to track the current operating system as well and provide these kinds of warnings / messages when appropriate.
Thanks,
Kevin