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I have the exact same issue, trying to compile 3.7.1 with a custom libffi location. Note that I must build libffi from source and can't install binaries provided by my distro, I believe this is the origin of the problem. Probably the python build system checks for libffi in some "standard" locations and it doesn't seem possible to use libffi from a custom location.
This is where libffi gets installed after passing --prefix=$HOME/opt to ./configure:
$HOME/opt/lib64/libffi.so.6.0.4
$HOME/opt/lib64/libffi.a
$HOME/opt/lib64/libffi.la
$HOME/opt/lib64/libffi.so.6
$HOME/opt/lib64/libffi.so
$HOME/opt/lib/pkgconfig/libffi.pc
$HOME/opt/lib/libffi-3.2.1/include/ffi.h
$HOME/opt/lib/libffi-3.2.1/include/ffitarget.h
$HOME/opt/share/info/libffi.info
In any case, just to be sure, I've copied the header files to
$HOME/opt/include/ffi.h
$HOME/opt/include/ffitarget.h
And pkg-config works:
[fetch@fetch opt]$ pkg-config --libs libffi
-L/home/fetch/opt/lib/../lib64 -lffi
[fetch@fetch opt]$ pkg-config --cflags libffi
-I/home/fetch/opt/lib/libffi-3.2.1/include
These environment variables are also set:
LD_LIBRARY_PATH=/home/fetch/opt/lib:/home/fetch/opt/lib64
C_INCLUDE_PATH=/home/fetch/opt/include
And still _ctypes fails to build (but python itself (minus _ctypes) compiles successful and works perfectly well).