i found the following in my configure generated by 
autoconf 2.13 & automake 1.4:

if test "`cd $srcdir && pwd`" != "`pwd`" && test -f $srcdir/config.status; then
  { echo "configure: error: source directory already configured; run "make distclean" 
there first" 1>&2; exit 1; }
fi
cat >> confdefs.h <<EOF
#define PACKAGE "$PACKAGE"
EOF

(note the " around "make distclean" - they should be \")

i guess, the offending macro is AM_INIT_AUTOMAKE.

best regards

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