This bug has been fixed in SVN.

Snapshots of the sources are packaged every three hours; this change
will be in the next snapshot. You can grab the snapshot at
http://snaps.php.net/.

 For Windows:

http://windows.php.net/snapshots/
 
Thank you for the report, and for helping us make PHP better.

thx for the patch

Had to dive a littl deeper because of cross-compileing php5.6.40 resulted, even ,with the patch, in a binary with unsupoorted extensions. Found that acincludes.m4-PHP_CHECK_FUNC_LIB cant compile its test in the cross-compile environment an so opts out with found=no reverting any other choice made before.

Test:
--- acinclude.m4
+++ acinclude.m4
@@ -1904,10 +1904,11 @@
     AC_CHECK_LIB($2, __$1, [found=yes], [found=no])
   ])
 
+  // Add the opportunity to define how PHP_CHECK_FUNC_LIB handles a cross-build in configure.in
   if test "$found" = "yes"; then
     ac_libs=$LIBS
     LIBS="$LIBS -l$2"
-    AC_TRY_RUN([main() { return (0); }],[found=yes],[found=no],[found=no])
+    AC_TRY_RUN([main() { return (0); }],[found=yes],[found=no],[found=$with_freetz_fix_cross])
     LIBS=$ac_libs
   fi

--- configure.in
+++ configure.in
@@ -453,10 +453,14 @@
 PHP_CHECK_FUNC(gethostbyaddr, nsl)
 PHP_CHECK_FUNC(yp_get_default_domain, nsl)
 
+# PHP_CHECK_FUNC->_AC_CHECK_FUNC->PHP_CHECK_FUNC_LIB
+# Define how to call AC_TRY_RUN in PHP_CHECK_FUNC_LIB when cross-compiling")
+$with_freetz_fix_cross=yes
 PHP_CHECK_FUNC(dlopen, dl)
 if test "$ac_cv_func_dlopen" = "yes"; then
   AC_DEFINE(HAVE_LIBDL, 1, [ ])
 fi
+$with_freetz_fix_cross=no
 AC_CHECK_LIB(m, sin)
 
 dnl Check for inet_aton

have a nice day,
Marcedo