I've been able to successfully install and patch dfu-programmer now, thanks to the information you've provided. Thanks.
Unfortunately I'm still having trouble flashing firmware. When I short the two pins on the ISP header closest to the USB port in order to put the Uno r3 16u2 into DFU mode, the serial port in the native Arduino IDE goes away. So, I am relatively certain the board is in DFU mode.
However, when I run sudo dfu-programmer at90162 erase I still get the error dfu-programmer: no device present.
I have the menu for dfu programmer printing, as well as the menu from Macports, which can be seen here:
Adam-Rolphs-iMac-3:~ adamrolph$ port search libusb
libusb @1.0.9 (devel)
library for USB device access
libusb-compat @0.1.4 (devel)
library for USB device access
libusb-devel @1.0.8.20101017 (devel)
library for USB device access
libusb-legacy @0.1.12 (devel)
Library providing access to USB devices
Found 4 ports.
This post by member Stimmer may be helpful to me but I do not know how to run the commands mentioned in it:
Both dmesg and lsusb should confirm the device mode change. If there's just a reset without a mode change dmesg should confirm that too.
Any help is appreciated thank you.