flashing arduino firmware (avrdude) fails due to Serial.print() statements

Official Hardware Classic Yún
1

I have an arduino sketch loaded that prints the string "blink" everytime the led blinks. When I attempt to flash new firmware to the arduino using the 1.5.7 IDE over USB, I get an error that contains some of the print statement as replies to avrdude. Is it possible that some sort of reset is not happening correctly on the arduino chip?

avrdude: Version 6.0.1, compiled on Apr 3 2014 at 22:00:33
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2009 Joerg Wunsch

System wide configuration file is "/Applications/Arduino.app/Contents/Resources/Java/hardware/tools/avr/etc/avrdude.conf"
User configuration file is "/Users/topaz/.avrduderc"
User configuration file does not exist or is not a regular file, skipping

Using Port : /dev/tty.usbmodem1d21
Using Programmer : avr109
Overriding Baud Rate : 57600
AVR Part : ATmega32U4
Chip Erase delay : 9000 us
PAGEL : PD7
BS2 : PA0
RESET disposition : dedicated
RETRY pulse : SCK
serial program mode : yes
parallel program mode : yes
Timeout : 200
StabDelay : 100
CmdexeDelay : 25
SyncLoops : 32
ByteDelay : 0
PollIndex : 3
PollValue : 0x53
Memory Detail :

Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

eeprom 65 20 4 0 no 1024 4 0 9000 9000 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

flash 65 6 128 0 yes 32768 128 256 4500 4500 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

lfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

hfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

efuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

lock 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00

Programmer Type : butterfly
Description : Atmel AppNote AVR109 Boot Loader

Connecting to programmer: .avrdude: Send: . [1b]
avrdude: Send: S [53]
avrdude: Recv: b [62]

avrdude: Recv: l [6c] i [69] n [6e] k [6b] . [0d] . [0a]
avrdude: Send: V [56]
avrdude: Recv: b [62] l [6c]
avrdude: Send: v [76]
avrdude: Recv: i [69]
avrdude: Recv: n [6e]
avrdude: Send: p [70]
avrdude: Recv: k [6b]
Found programmer: Id = "blink
"; type = k
Software Version = b.l; Hardware Version = i.n
avrdude: Send: a [61]
avrdude: Recv: . [0d]
avrdude: Send: b [62]
avrdude: Recv: . [0a]
avrdude: error: buffered memory access not supported. Maybe it isn't
a butterfly/AVR109 but a AVR910 device?

2

Yes, that is possible.
The DTR pin is connected via 100nF to the reset.

There is another possibility:
Suppose you have uploaded your sketch without bootloader, and you send far too many data to the serial port. That could cause it.
Perhaps if you do have the normal bootloader, and start immediately to spit out too much serial data, that might bully avrdude.

What you can do:
Don't use the avrdude command line, you might have overlooked an option. Use the Arduino IDE.
Open the serial monitor a few times, does that cause a reset ? If not, check the hardware.
You can try to press reset yourself, and try to find the soft spot where avrdude is connecting just after the reset.
If the reset hardware is okay, and nothing seems possible. Try a programmer via the ICSP header and re-write the bootloader.

After writing this post, I noticed this is for the Yun. What I wrote above is for the Uno.