For some reason I cannot find the original post, so I'll just post here.

Right after a svn co:
...
U freeciv
Checked out revision 19424.
[11:13:ttypd][akfaew@spock:~/longturn:34]$ cd freeciv/
[11:13:ttypd][akfaew@spock:~/longturn/freeciv:35]$ ./autogen.sh --disable-client --enable-server --enable-auth
+ checking for autoconf >= 2.58 ... found 2.65, ok.
+ checking for autoheader >= 2.58 ... found 2.65, ok.
+ checking for automake >= 1.7 ... found 1.9.6, ok.
+ checking for aclocal >= 1.7 ... found 1.9.6, ok.
+ checking for libtoolize >= 1.4.3 ... found 1.5.26, ok.
+ checking for xgettext >= 0.10.36 ... found 0.18.1, ok.
+ checking for msgfmt >= 0.10.36 ... found 0.18.1, ok.
+ running /usr/local/bin/aclocal-1.9 ...
+ running /usr/local/bin/autoheader-2.65 ...
+ running /usr/local/bin/autoconf-2.65 ...
configure.ac:64: error: possibly undefined macro: AM_INIT_AUTOMAKE
If this token and others are legitimate, please use m4_pattern_allow.
See the Autoconf documentation.
configure.ac:127: error: possibly undefined macro: AM_CONDITIONAL
configure.ac:135: error: possibly undefined macro: AC_MSG_ERROR
configure.ac:385: error: possibly undefined macro: AC_DISABLE_SHARED
configure.ac:386: error: possibly undefined macro: AC_PROG_LIBTOOL
configure.ac:402: error: possibly undefined macro: AM_ICONV
configure.ac:403: error: possibly undefined macro: AM_LIBCHARSET
configure.ac:404: error: possibly undefined macro: AM_LANGINFO_CODESET
configure.ac:437: error: possibly undefined macro: AM_GLIB_GNU_GETTEXT
configure.ac:553: error: possibly undefined macro: AC_C99_VARIADIC_MACROS
configure.ac:554: error: possibly undefined macro: AC_C99_VARIABLE_ARRAYS
configure.ac:555: error: possibly undefined macro: AC_C99_INITIALIZERS
configure.ac:556: error: possibly undefined macro: AC_C99_STDINT_H
configure.ac:830: error: possibly undefined macro: AC_GGZ_CHECK
configure.ac:950: error: possibly undefined macro: AC_FUNC_VSNPRINTF

/usr/local/bin/autoconf-2.65 failed

Then immediately after that:
[11:45:ttypd][akfaew@spock:~/longturn/freeciv:36]$ ./autogen.sh --disable-client --enable-server --enable-auth
+ checking for autoconf >= 2.58 ... found 2.65, ok.
+ checking for autoheader >= 2.58 ... found 2.65, ok.
+ checking for automake >= 1.7 ... found 1.9.6, ok.
+ checking for aclocal >= 1.7 ... found 1.9.6, ok.
+ checking for libtoolize >= 1.4.3 ... found 1.5.26, ok.
+ checking for xgettext >= 0.10.36 ... found 0.18.1, ok.
+ checking for msgfmt >= 0.10.36 ... found 0.18.1, ok.
+ running /usr/local/bin/aclocal-1.9 ...
+ running /usr/local/bin/autoheader-2.65 ...
+ running /usr/local/bin/autoconf-2.65 ...
+ running libtoolize ...
You should add the contents of `/usr/local/share/aclocal/libtool.m4' to `aclocal.m4'.
Putting files in AC_CONFIG_AUX_DIR, `bootstrap'.
+ running /usr/local/bin/automake-1.9 ...
Use of uninitialized value $macro in string eq at /usr/local/bin/automake-1.9 line 4673, <GEN0> line 1.
Use of uninitialized value $macro in exists at /usr/local/bin/automake-1.9 line 4675, <GEN0> line 1.
Use of uninitialized value $macro in concatenation (.) or string at /usr/local/bin/automake-1.9 line 4675, <GEN0> line 1.
automake-1.9: ####################
automake-1.9: ## Internal Error ##
automake-1.9: ####################
automake-1.9: unrequested trace `'
automake-1.9: Please contact <bug-automake@gnu.org>.
at /usr/local/share/automake-1.9/Automake/Channels.pm line 562
Automake::Channels::msg('automake', '', 'unrequested trace `\'') called at /usr/local/share/automake-1.9/Automake/ChannelDefs.pm line 191
Automake::ChannelDefs::prog_error('unrequested trace `\'') called at /usr/local/bin/automake-1.9 line 4675
Automake::scan_autoconf_traces('configure.ac') called at /usr/local/bin/automake-1.9 line 4877
Automake::scan_autoconf_files() called at /usr/local/bin/automake-1.9 line 7493

/usr/local/bin/automake-1.9 failed

The second autogen fails for another reason but svn stat and svn diff show nothing.