We have to modify the configure.ac or configure.in file and delete the check which is causing problems. Cross compiling with autoconf is pretty tricky and usually needs some tweaking of the config files or makefiles to work.
or we can echo variant into .cache file, such as:
echo ac_cv_type_long_long=yes>$ARCH-linux.cache
and then run configure as:
./configure --host=$ARCH-linux --prefix=$ROOTFS_DIR/usr --cache-file=$ARCH-linux.cache