nauty: disable native code (illegal instructions)

[tornaria]

The package currently shipped in void gives me illegal instructions in a
nehalem cpu.

This commit fixes the issue by disabling native compilation unless a build
option is given; also disable popcnt which, although available on nehalem, is
not available in baseline x86_64.

An easy way to spot the issue is to run something like:

$ geng 2
>A geng -d0D1 n=2 e=0-1
Illegal instruction

Testing the changes

• I tested the changes in this PR: YES

I compiled with ./xbps-src build nauty on a cascade lake cpu, then run ./xbps-src check nauty on a nehalem cpu. This breaks before the present PR, and works ok after.

I also tested sagemath: previously I was getting a lot of doctest failures which are now fixed.

Cc: @leahneukirchen please merge this before sagemath.