Thanks for the report.  This warning is currently visible on many/all of the buildbots on all branches.  The conflict is caused by the upgrade of the bundled to libexpat to version 2.2.1 (bpo-30694). 2.2.1 introduced a define of _GNU_SOURCE into Modules/expat/xmlparse.c.  The definition in xmlparse is simply:

#define _GNU_SOURCE

But Python, in pyconfig.h, which ./configure generates from pyconfig.h.in, may already have defined _GNU_SOURCE thusly:

#define _GNU_SOURCE 1

pyconfig.h gets included into our copy of Modules/expat/expat_config.h which is included later in xmlparse.c causing the compile warning.

The simplest way to avoid the warning is to just change the definition in xmlparse.c to match that in pyconfig.h; the compilers don't complain if the definition is identical.  I have now merged that fix into the 3.6 branch so builders of 3.6.2 won't see the warning.  I will leave this open for @haypo to review and to handle merging into the other branches affected by bpo-30694 (master, 3.5, 2.7, 3.4, 3.3).