My main gripe with autotools these days is that there seems to be no standard mechanism for specifying non-standard locations for dependencies. (Or if there is, that no packages use it...) If I build something from source, it is nearly always because I want a newer version than what is available from the appropriate package repositories, which usually means that I will want newer versions of the dependencies too, or because I want a built-from-source version of one of those dependencies. If I'm really lucky, pkg-config will pick them up. Sometimes just setting LDFLAGS=-L/my/build CPPFLAGS=-I/my/build will work. Sometimes I have to say --with-gnomovision=/my/build, sometimes I will have to say --with-gnomovision-includes=/my/build/include, ...