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Other things Automake recognizes

Every time Automake is run it calls Autoconf to trace configure.in. This way it can recognize the use of certain macros and tailor the generated Makefile.in appropriately. Currently recognized macros and their effects are:

AC_CONFIG_HEADERS
Automake will generate rules to rebuild these headers. Older versions of Automake required the use of AM_CONFIG_HEADER (see Macros); this is no longer the case today.
AC_CONFIG_AUX_DIR
Automake will look for various helper scripts, such as mkinstalldirs, in the directory named in this macro invocation. (The full list of scripts is: config.guess, config.sub, depcomp, elisp-comp, compile, install-sh, ltmain.sh, mdate-sh, missing, mkinstalldirs, py-compile, texinfo.tex, and ylwrap.) Not all scripts are always searched for; some scripts will only be sought if the generated Makefile.in requires them.

If AC_CONFIG_AUX_DIR is not given, the scripts are looked for in their standard locations. For mdate-sh, texinfo.tex, and ylwrap, the standard location is the source directory corresponding to the current Makefile.am. For the rest, the standard location is the first one of ., .., or ../.. (relative to the top source directory) that provides any one of the helper scripts. See Finding `configure' Input.

Required files from AC_CONFIG_AUX_DIR are automatically distributed, even if there is no Makefile.am in this directory.

AC_CANONICAL_HOST
Automake will ensure that config.guess and config.sub exist. Also, the Makefile variables host_alias and host_triplet are introduced. See Getting the Canonical System Type.
AC_CANONICAL_SYSTEM
This is similar to AC_CANONICAL_HOST, but also defines the Makefile variables build_alias and target_alias. See Getting the Canonical System Type.
AC_LIBSOURCE
AC_LIBSOURCES
AC_LIBOBJ
Automake will automatically distribute any file listed in AC_LIBSOURCE or AC_LIBSOURCES.

Note that the AC_LIBOBJ macro calls AC_LIBSOURCE. So if an Autoconf macro is documented to call AC_LIBOBJ([file]), then file.c will be distributed automatically by Automake. This encompasses many macros like AC_FUNC_ALLOCA, AC_FUNC_MEMCMP, AC_REPLACE_FUNCS, and others.

By the way, direct assignments to LIBOBJS are no longer supported. You should always use AC_LIBOBJ for this purpose. See AC_LIBOBJ vs. LIBOBJS.

AC_PROG_RANLIB
This is required if any libraries are built in the package. See Particular Program Checks.
AC_PROG_CXX
This is required if any C++ source is included. See Particular Program Checks.
AC_PROG_F77
This is required if any Fortran 77 source is included. This macro is distributed with Autoconf version 2.13 and later. See Particular Program Checks.
AC_F77_LIBRARY_LDFLAGS
This is required for programs and shared libraries that are a mixture of languages that include Fortran 77 (see Mixing Fortran 77 With C and C++). See Autoconf macros supplied with Automake.
AC_PROG_LIBTOOL
Automake will turn on processing for libtool (see Introduction).
AC_PROG_YACC
If a Yacc source file is seen, then you must either use this macro or define the variable YACC in configure.in. The former is preferred (see Particular Program Checks).
AC_PROG_LEX
If a Lex source file is seen, then this macro must be used. See Particular Program Checks.
AC_SUBST
The first argument is automatically defined as a variable in each generated Makefile.in. See Setting Output Variables.

If the Autoconf manual says that a macro calls AC_SUBST for var, or defined the output variable var then var will be defined in each generated Makefile.in. E.g. AC_PATH_XTRA defines X_CFLAGS and X_LIBS, so you can use the variable in any Makefile.am if AC_PATH_XTRA is called.

AM_C_PROTOTYPES
This is required when using automatic de-ANSI-fication; see ANSI.
AM_GNU_GETTEXT
This macro is required for packages which use GNU gettext (see gettext). It is distributed with gettext. If Automake sees this macro it ensures that the package meets some of gettext's requirements.
AM_MAINTAINER_MODE
This macro adds a --enable-maintainer-mode option to configure. If this is used, automake will cause maintainer-only rules to be turned off by default in the generated Makefile.ins. This macro defines the MAINTAINER_MODE conditional, which you can use in your own Makefile.am.