Perhaps it's useful to report which are the offending lines in the build log. For Trilinos [1], for example, a hidden flags are reported, but I have no idea why. Can you help me out?
Cheers, Nico [1] https://buildd.debian.org/status/fetch.php?pkg=trilinos&arch=amd64&ver=12.12.1-5&stamp=1517856320&raw=0