EMBOSS configure looks for gcc and uses this of preference when compiling EMBOSS. This is not ideal for those who wish to have a compiled and linked 64bit version of EMBOSS. The current version is NOT 64 bit clean (ie. it does not necessarily use 64 bit representation internally) but will compile and run quite happily on 64 bit systems.
Additional notes are appended below for the various operating systems we have information on.