clockmaker should build ntpsec from a release, not tip-of-tree
I recently used clockmaker to set up a Pi 3B+ server with an Uputronics GPS board, and the only problem I had was that the following line failed:
./waf configure --refclock=nmea,pps,shm,gpsd
git bisect revealed this was caused by commit 7b62c4bd8d47a14ed279f1e4183a3452b3c0dd6b. I checked out the most recent tag (NTPsec_1_1_3), and was able to successfully build and configure my server.