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In the end I did the following and it seems to have worked:

I went here: http://www.cecm.sfu.ca/sage/spkg/upstream/gap_packages/index.html and downloaded the version of GAP 4.10 from there that already has io and orb and digraphs in it. Then I replaced the gap folder in /Applications/SageMath/local/share/ with this new gap folder. I opened a terminal at this new gap folder and ran "./configure" and then "make". Then I opened a terminal at the io folder inside this new gap folder and ran "./configure" and then "make", and then did the same at the digraphs folder.