(It fails from the main directory, but the output is shorter this way)
bead:CVS/lyx/src>make clean
Making clean in .
make[1]: Entering directory `/u2/karger/lyx/CVS/lyx/src'
test -z "lyx" || rm -f lyx
rm -f *.o core *.core
make[1]: Leaving directory `/u2/karger/lyx/CVS/lyx/src'
Making clean in encoding
make[1]: Entering directory `/u2/karger/lyx/CVS/lyx/src/encoding'
make[1]: *** No rule to make target `clean'. Stop.
make[1]: Leaving directory `/u2/karger/lyx/CVS/lyx/src/encoding'
make: *** [clean-recursive] Error 1
-Amir