The order in which configure.ac calls the Autoconf macros is not
important, with a few exceptions. Every configure.ac must
contain a call to AC_INIT before the checks, and a call to
AC_OUTPUT at the end (see Output). Additionally, some macros
rely on other macros having been called first, because they check
previously set values of some variables to decide what to do. These
macros are noted in the individual descriptions (see Existing Tests), and they also warn you when configure is created if they
are called out of order.
To encourage consistency, here is a suggested order for calling the Autoconf macros. Generally speaking, the things near the end of this list are those that could depend on things earlier in it. For example, library functions could be affected by types and libraries.
Autoconf requirements
AC_INIT(package, version, bug-report-address)
information on the package
checks for programs
checks for libraries
checks for header files
checks for types
checks for structures
checks for compiler characteristics
checks for library functions
checks for system services
AC_CONFIG_FILES([file...])
AC_OUTPUT