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I ran in this problem with piSNES as well. Here is how I fixed it:

Navigate to the source folder:
Edit the Makefile:
Find the line starting with “LDLIBS=”
Add to the end of this line depending on the error received
Example: if the error was about, make sure it has
“-lm” so the compile command knows to add the libm library.
or if it was for librt, add “-lrt”.
Save the Makefile
Compile again:
sudo make

It should compile at this point, or complain about another library. If it does, simply repeat these steps, substituting the new library.

This only corrects the symptoms. I don’t know why the makefile is not generated with the correct libraries.