I have an R package which is easily sped up by using OpenMP. If your compiler supports it then you get the win, if it doesn\'t then the pragmas are ignored and you get one core.
Just addressing your question regarding the usage of autoconf--no, you do not want to run autoconf with any arguments, nor should you redirect its output. You are correct that running autoconf to build the configure script is something that the package maintainer does, and the resulting configure script is distributed. Normally, to generate the configure script from configure.ac (older packages use the name configure.in, but that name has been discouraged for several years), the developer simply runs autoconf with no arguments. Before running autoconf, it is necessary to run aclocal, autoheader, libtoolize, etc... There is also a tool (autoreconf) which simplifies the process and invokes all the required programs in the correct order. It is now more typical to run autoreconf instead of autoconf.