If at first you don't succeed, try, try and try again. It is not uncommon to make typos or other mistakes when running
./configure. If you want to run configure again you should run
make cleanbefore running
./configurewith (hopefully) the correct options. With an earlier EMBOSS release, or as a developer with an earlier release of autoconf, you must first delete the file
config.cachebut this is no longer produced.