The tutorial at http://arduino.cc/playground/Code/Eclipse
states in the first paragraph: "There is an easier way to use Eclipse as explained on http://www.baeyens.it/eclipse/
Did you follow the instructions at www.baeyens.it
or the one on the playground?
The first one is that I have to push reset right at upload. I thought this was an older issue based on all the forum posts I have read on the web. I assumed it was fixed already. The instructions at the above URL, seem a little outdated when suggesting to download an executable. I tried it, but it was trying to load an older version of AVRDude. Any suggestions?
If you are using the arduino eclipse plugin and it can load the rxtx dll it should work in all cases. if it can't load the rxtx dll only the mega has an issue.
if you use the avrplugin make sure you use arduino as hardware setting in the avrdude settings. (unless you have a mega in which case you will still need to reset it manually)
My second issue is that when I upload the code from Eclipse (doing the manual reset timing), it uploads fine, but gives me this output. (This is partial)
avrdude: Device signature = 0x000000
avrdude: Yikes! Invalid device signature.
avrdude: Expected signature for ATMEGA328P is 1E 95 0F
avrdude: NOTE: FLASH memory has been specified, an erase cycle will be performed
To disable this feature, specify the -D option.
avrdude: erasing chip
avrdude: reading input file "CustomLEDPoi.hex"
avrdude: input file CustomLEDPoi.hex auto detected as Intel Hex
avrdude: writing flash (10082 bytes):
It says its successful at the end, but when I watch my LEDs that are hooked up, they light up very strangely, not following the uploaded code at all. I know that there is not an issue with my code, because I can upload the exact same code just fine using the Arduino IDE. The LEDs behave correctly then. The LED setup I have is similar to this example: http://www.arduino.cc/en/Tutorial/ShiftOut
The avrdude warnings are warning and there is nothing wrong there. As it uploaded a sketch and you don't see the board doing what you think it should do I only see 2 options
1) AvrDude is not uploading the sketch you think it should upload.
2) Compilation doesn't use the input you think it does.
Therefore I consider following questions:
if there are multiple configurations; are you always using the same one?
Have you saved your files in eclipse before compiling? (very common mistake)
Have you successfully compiled?