I tried to compile Mozilla Thunderbird last night. Since it takes awhile I let it run overnight. This morning I saw that it failed to compile. I looked into it and it appeared that an executable was missing, but I couldn't figure out why so I manually ran through the last few steps in the compile log. Well it turns out SONAR didn't like one of the executables created and used during the compilation process and simply deleted it. The executable creates a hash file and signs other executables for security purposes.
Basically SONAR ruined the compile and I have to start over from scratch. Of course there's no way to exclude programs from SONAR until they're actually deleted so hopefully SONAR won't delete other programs the next time I try to compile.