Using Stepan Kasal's advice (adjusting configure.in for _really_ integrated sub-packages and separating out not-really integrated ones), I managed to avoid the warning when aclocal.m4 is created (see <http://article.gmane.org/gmane.comp.sysutils.automake.general:6150>) Thanks to all who replied!
Unfortunately, the more insidious problem persists: cd modules/regexp; autoconf --include=/cygdrive/d/gnu/clisp/current/src/autoconf --include=/cygdrive/d/gnu/clisp/current configure:6028: error: possibly undefined macro: AC_CHECK_HEADERS_ONCE If this token and others are legitimate, please use m4_pattern_allow. See the Autoconf documentation. configure:6029: error: possibly undefined macro: AC_CHECK_FUNCS_ONCE make: *** [modules/regexp/configure] Error 1 this is because src/m4/onceonly.m4 (that defines AC_CHECK_FUNCS_ONCE &c) is not included into src/autoconf/aclocal.m4 (when I do $ cat m4/onceonly.m4>>autoconf/aclocal.m4 it works, of course). So, the question is: why isn't onceonly.m4 appended to aclocal.m4? Again, aclocal.m4 is created by $ aclocal -I `pwd`/src/m4 --output=src/autoconf/aclocal.m4 Thanks! -- Sam Steingold (http://www.podval.org/~sds) running w2k <http://www.camera.org> <http://ffii.org/> <http://pmw.org.il/> <http://www.palestinefacts.org/> <http://www.mideasttruth.com/> Parachute for sale, used once, never opened, small stain.