This is caused by _GNU_SOURCE being defined here: https://github.com/python/cpython/blob/c08177a1ccad2ed0d50898c2731b518c631aed14/configure.ac#L124, But also getting defined by AC_USE_SYSTEM_EXTENSIONS (https://github.com/python/cpython/blob/c08177a1ccad2ed0d50898c2731b518c631aed14/configure.ac#L906).

AC_USE_SYSTEM_EXTENSIONS does use an #ifndef but Python's AC_DEFINE seems to be getting order after it.

New changeset 05b72ede95521b2d897cb4c7b034139b5437c592 by Ned Deily in branch '3.6':
bpo-30797, bpo-30694: Avoid _GNU_SOURCE redefined warning in xmlparse.c (#2615)
https://github.com/python/cpython/commit/05b72ede95521b2d897cb4c7b034139b5437c592

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).

One more thing: building with a recent gcc on Linux:
$ gcc --version
gcc (Debian 6.3.0-18) 6.3.0 20170516

also gives an "unused but set variable" warning.

./Modules/expat/xmlparse.c: In function ‘gather_time_entropy’:
./Modules/expat/xmlparse.c:780:7: warning: variable ‘gettimeofday_res’ set but not used [-Wunused-but-set-variable]
   int gettimeofday_res;
       ^~~~~~~~~~~~~~~~

Since I didn't see it in time, I didn't try to fix this for 3.6.2 but it would be best to silence it going forward.

New changeset bdabd7666032ce356d550da21c35e4bee5b3448c by Ned Deily in branch '3.6':
bpo-30797, bpo-30694: Avoid _GNU_SOURCE redefined warning in xmlparse.c (#2615)
https://github.com/python/cpython/commit/bdabd7666032ce356d550da21c35e4bee5b3448c

New changeset 884c4ca33ab84b9fc57338cf59f79e0436d3da43 by Victor Stinner (Segev Finer) in branch '2.7':
[2.7] bpo-30797: Avoid _GNU_SOURCE redefined warning in xmlparse.c (GH-2670) (#2672)
https://github.com/python/cpython/commit/884c4ca33ab84b9fc57338cf59f79e0436d3da43

The fix is now in 3.5-3.7 and 2.7, unless you intend to also back port to 3.4 and 3.3, this can be closed.