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Given the error message in

>./factor 2006
/usr/bin/env: sage -python: No such file or directory

It looks like "sage" can't be found, so I would guess that you haven't followed this direction from the tutorial:

In order to use this script, your SAGE_ROOT must be in your PATH.

I don't know how to do this using VirtualBox, but it might be this: find the directory SAGE_ROOT where sage is; say it's "/home/user/sage-5.3/". Then do

> export PATH=/home/user/sage-5.3/:$PATH

(There should be exactly one space in this line, between "export" and "PATH".) Then try

> ./factor 2006