root@arren-mining:/home/arren/cuda-extract/cudaminer-2014-02-28/cudaminer-src-2014.02.28# ./autogen.sh && ./configure && make
./autogen.sh: line 1: $'autoconf\r': command not found
root@arren-mining:/home/arren/cuda-extract/cudaminer-2014-02-28/cudaminer-src-2014.02.28#
Execute this in a terminal:
sudo apt-get install automake
This should install automake and its dependencies, which include autoconf. This does not include gcc, CUDA toolkit, or other libraries which you may need. You did not specify whether you followed the README.txt guide that directed you to install those dependencies so I have omitted them.