Same error, on OS X Mavericks:

checking for sysvipc shared memory support... no
checking for mmap() using MAP_ANON shared memory support... no
checking for mmap() using /dev/zero shared memory support... no
checking for mmap() using shm_open() shared memory support... no
checking for mmap() using regular file shared memory support... no
checking "whether flock struct is linux ordered"... "no"
checking "whether flock struct is BSD ordered"... "no"
configure: error: Don't know how to define struct flock on this system, set --enable-opcache=no

Same problem.

In ZendAccelerator.h it looks for the presence of other defines such as __linux__ first to determine flock order, in favor of the results of the test (HAVE_FLOCK_LINUX)
So why is not being able to run the test fatal?


==
# if defined(__FreeBSD__) || defined(__FreeBSD_kernel__) || (defined(__APPLE__) && defined(__MACH__)/* Darwin */) || defined(__OpenBSD__) || defined(__NetBSD__)
#  define FLOCK_STRUCTURE(name, type, whence, start, len) \
		struct flock name = {start, len, -1, type, whence}
# elif defined(__svr4__)
#  define FLOCK_STRUCTURE(name, type, whence, start, len) \
		struct flock name = {type, whence, start, len}
# elif defined(__linux__) || defined(__hpux) || defined(__GNU__)
#  define FLOCK_STRUCTURE(name, type, whence, start, len) \
		struct flock name = {type, whence, start, len, 0}
# elif defined(_AIX)
#  if defined(_LARGE_FILES) || defined(__64BIT__)
#   define FLOCK_STRUCTURE(name, type, whence, start, len) \
		struct flock name = {type, whence, 0, 0, 0, start, len }
#  else
#   define FLOCK_STRUCTURE(name, type, whence, start, len) \
		struct flock name = {type, whence, start, len}
#  endif
# elif defined(HAVE_FLOCK_BSD)
#  define FLOCK_STRUCTURE(name, type, whence, start, len) \
		struct flock name = {start, len, -1, type, whence}
# elif defined(HAVE_FLOCK_LINUX)
#  define FLOCK_STRUCTURE(name, type, whence, start, len) \
		struct flock name = {type, whence, start, len}
# else
#  error "Don't know how to define struct flock"
# endif
#endif
==

"checking "whether flock struct is linux ordered"... "no"
checking "whether flock struct is BSD ordered"... "no"
configure: error: Don't know how to define struct flock on this system, set --enable-opcache=no"

I had the same error, while compiling PHP (5.6.4, but that does not matter, because I tried als PHP 5.6.3 and was reproducable) on Debian GNU/Linux. I saw that problem when I forgot to set LD_LIBRARY_PATH environment variable.

So doing it like that solved my problem:

$ export LD_LIBRARY_PATH=/usr/local/mysql/lib
$ ./configure --enable-fpm --with-mcrypt --with-zlib --with-curl --disable-debug --disable-rpath --enable-inline-optimization --with-bz2 --enable-sockets --enable-zip --with-fpm-user=www-data --with-fpm-group=www-data --with-mysql=/usr/local/mysql/
$ make
$ make test
# export LD_LIBRARY_PATH=/usr/local/mysql/lib
# make install

Fails with PHP 7.0.2/OpenWRT as well, and disabling opcache isn't an acceptable option as the enhanced opcache performance is a major reason to want PHP 7.

Obviously the test program can't be run in a cross-compile - the configure script should be modified to take flock_type as an input variable to support cross-compiling. If the input variable is set then don't bother with the test program.

all of these cross-compilation problems could easily be solved if php would use the cache variables feature for these variables as well so user can easily override the test from the commandline.
example:

./configure ac_cv_crypt_SHA512=yes ac_cv_linux_lock=yes

however due to lack of it, you need to either patch the configure script, or the configure.ac and rerun all the autoreconf stuff which is highly error prone due to all the involved m4 macros and different tool versions.

note that the cache variable is used for the above SHA512 crypt check

$as_echo_n "checking for SHA512 crypt... " >&6; }
if ${ac_cv_crypt_sha512+:} false; then :
  $as_echo_n "(cached) " >&6                                                    
else

if test "$cross_compiling" = yes; then :                                        

  ac_cv_crypt_sha512=no

else
  cat confdefs.h - <<_ACEOF >conftest.$ac_ext                                   


but not for this check, the one for strcasestr and probably others.
for comparison:

  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for strcasestr" >&5         
$as_echo_n "checking for strcasestr... " >&6; }                                 
  if test "$cross_compiling" = yes; then :                                      
  { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5         
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}                                  
as_fn_error $? "cannot run test program while cross compiling                   
See \`config.log' for more details" "$LINENO" 5; }                              
else                                                                            
  cat confdefs.h - <<_ACEOF >conftest.$ac_ext

little reminder: 3 years later, as of 2016 and PHP 7.0.10, there are still 3 configure checks that cannot be worked around without patching configure:

1) check for strcasestr
2) this one here
3) pthreads_working. if crosscompiling, and the system is not netware, it is assumed that pthread are broken.
i think if a test compile with link against -lpthread works, it can be assumed that pthreads work. most likely the lib is there for a reason.
they all could be *easily* fixed by enabling a cache variable that the user can set.

The problematic flock check has been removed in PHP 7.2 via https://github.com/php/php-src/commit/9222702633c63254b08466b322266b647ac3e905.