In configure.ac: AC_OUTPUT([Makefile examples/Makefile examples/transition_state_search2/Makefile examples/transition_state_search2/carbocation_rearrangement_hydride_shift/Makefile examples/transition_state_search2/carbocation_rearrangement_methide_shift/Makefile examples/transition_state_search2/cycloaddition_Diels-Alder/Makefile examples/transition_state_search2/E2-reaction/Makefile examples/transition_state_search2/sigmatropic_rearrangement_Cope/Makefile examples/transition_state_search2/SN2-reaction/Makefile examples/transition_state_search2/tautomeric_shift_keto_enol/Makefile src/Makefile]) the examples/* are making autconf barf: acinclude.m4:38: warning: underquoted definition of AM_SANITY_CHECK run info '(automake)Extending aclocal' or see http://sources.redhat.com/automake/automake.html#Extending-aclocal /usr/share/aclocal/wxwin.m4:36: warning: underquoted definition of AM_OPTIONS_WXCONFIG /usr/share/aclocal/wxwin.m4:59: warning: underquoted definition of AM_PATH_WXCONFIG /usr/share/aclocal/libglade.m4:7: warning: underquoted definition of AM_PATH_LIBGLADE configure.ac:150: required file `examples/Makefile.in' not found configure.ac:150: required file `examples/transition_state_search2/Makefile.in' not found configure.ac:150: required file `examples/transition_state_search2/carbocation_rearrangement_hydride_shift/Makefile.in' not found configure.ac:150: required file `examples/transition_state_search2/carbocation_rearrangement_methide_shift/Makefile.in' not found configure.ac:150: required file `examples/transition_state_search2/cycloaddition_Diels-Alder/Makefile.in' not found configure.ac:150: required file `examples/transition_state_search2/E2-reaction/Makefile.in' not found configure.ac:150: required file `examples/transition_state_search2/sigmatropic_rearrangement_Cope/Makefile.in' not found configure.ac:150: required file `examples/transition_state_search2/SN2-reaction/Makefile.in' not found configure.ac:150: required file `examples/transition_state_search2/tautomeric_shift_keto_enol/Makefile.in' not found autoreconf-2.59: automake failed with exit status: 1