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Alright, I do not know why, but it appears some .pc files in ~/ros_catkin_ws/install_isolated/lib/pkgconfig contained links to libraries in the form of :

-l:/path/to/lib/lib.dylib

While it should have been :

-l/path/to/lib/lib.dylib

(minus the ':'). I removed all the ':' from these pc files and that fixed it. Perhaps I should open a ticket?

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