I have two Dues. Neither of them will accept an upload on either the programming port or the USB port. I have the IDE v. 1.6.5 (r5) installed and the Due board information.
The ON and L LEDs are lit. I don't see any activity on the TX or RX leds near them.
The RX by the programming port flashes on one board when first powered on and the cable is plugged into the programming port.
The last line in the IDE console is:
Forcing reset using 1200bps open/close on port /dev/ttyACM2
/home//.arduino15/packages/arduino/tools/bossac/1.3a-arduino/bossac -i -d --port=ttyACM2 -U false -e -w -v -b /tmp/build1362427682969201347.tmp/TimingTest.cpp.bin -R
After that, nothing.
I tried both the bossa gui and bossash. Both hang trying to do a USB scan.
As a test run Arduino IDE sudo to see if what is happening is a permissions issue. If so then look up online how to give your user account the proper permission to access serial devices.
I use 1.6.5, also on kubuntu 14.04. For me it works.
Apparently it uses another version bossac:
~/.arduino15/packages/arduino/tools/bossac/1.6-arduino/bossac
Maybe upgrade the ide?
I must add though that I have problems with the 1.6.4 version of the sam package. I can upload, but the sketch (e.g.blink) does not seem to run. No idea why. I dowgraded to 1.6.3, that fixed it.
My Due (actually an Itead "derivative" board) refuses to upload without a manual reset "near" the time of upload, and doesn't seem to start the sketch without an additional reset... (This on the "programming" port; the native usb port didn't work either, but I haven't expended any effort to get it working, either.)
Forcing reset using 1200bps open/close
I thought that this was a "thing" only on native USB ports, and that the "programming port" ran the same basic usb/serial code as the other 16u2 chips. Perhaps not...
I have a work around but it's weird. I'll rehash all the details.
I'm on Ubuntu 14.04 with Arduino IDE 1.6.5r5. I've got a Due board but I cannot upload programs to it. The bossa program just hangs in the IDE and also on the command line if I try it there.
I've been searching all over the web for ideas. I finally decided to try the Atmel SAM programmer to see what would happen. Maybe the boot loader / programmer / whatever was corrupted and this might fix it.
I installed it and ran it. Nothing. The little dialog just goes away when I say connect. I had the Arduino IDE running at the same time and it was on a stuck upload. The upload suddenly started running and I can see it giving percentage of upload. What??
I couldn't tell if the program was running. So I switched to the standard Blink example and went through the process again. Start the upload and then start the Atmel SAM programmer. It uploads and I get blinky, blinky, blinky.
I installed the IDE on a Windows XP system. It uploads sketches to the DUE without any problem.
For an unrelated reason, I created a new workspace for Eclipse for Arduino work. I'm using the plug-in for Arduino development.
I loaded the BlinkWithoutPause into Eclipse. It uploads to both the Programming and User port fine. The upload from the User port runs. The upload from Programming does not. I can see the TX/RX LEDs flashing and the verification says its good.