Oh crap it's back. This seems to happen not initially, but after gmake automatically decides to re-run configuref
config.status: error: in `/home/user/src/bitcoin':
config.status: error: Something went wrong bootstrapping makefile fragments
for automatic dependency tracking. If GNU make was not used, consider
re-running the configure script with MAKE="gmake" (or whatever is
necessary). You can also try re-running configure with the
'--disable-dependency-tracking' option to at least be able to build
the package (albeit without support for automatic dependency tracking).
See `config.log' for more details
gmake: *** [Makefile:718: Makefile] Error 1
Using --disable-dependency-tracking is an extremely bad idea because it essentially removes make's ability to detect what files are affected by changes during development or when pulling from git. This means you can get 'fault ines' where one side of the binary is compiled against a certain data structure and another with the changed one. This has resulted in hours of debugging headaches for me. Dont' do it.