There are 3 problems which cause the failure.

1. AC_CHECK_HEADERS(net/if_var.h) does not work on FreeBSD because 3 other headers need to be included first. I change it to AC_CHECK_HEADERS(net/if_var.h,,,[
+#include <net/if.h>
+#include <sys/types.h>
+#include <sys/socket.h>]) and solve the problem.

2. __FreeBSD_kernel_version is used in sysdeps/freebsd/open.c, but FreeBSD 9 and 10 only define __FreeBSD_version. Removing the __FreeBSD_kernel__ check can solve the problem.

3. There is a strange error when running g-ir-scanner. I don't know how to fix it.
Error closing file: No error: 0
Command '['/home/lantw44/gnome/source/libgtop/lib/tmp-introspect1hZkz0/GTop-2.0', '--introspect-dump=/home/lantw44/gnome/source/libgtop/lib/tmp-introspect1hZkz0/functions.txt,/home/lantw44/gnome/source/libgtop/lib/tmp-introspect1hZkz0/dump.xml']' returned non-zero exit status 1
gmake[3]: *** [GTop-2.0.gir] Error 1
gmake[3]: Leaving directory `/home/lantw44/gnome/source/libgtop/lib'