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Fragment of a discussion from Talk:BeagleBone Black Extracting eMMC contents
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Interesting, I just got the Element 14 Rev C board and didn't see this problem. I did have to use the barrel jack though, and had the other issues I mentioned.

15:27, 31 December 2014

I think in this case you are using the S2 button to boot completely off the SD card and thereby getting a consistent U-Boot image. I'm just sticking the card in an powering up the board, which relies on the U-Boot image loaded on the eMMC. There's not a strong reason to do that except that booting without S2 is simpler and does not require using the barrel jack.

12:57, 2 January 2015

Ah, got it; thanks for the clarification -- I didn't realize you could bypass the S2 and barrel by doing it this way. This is handy :)

18:51, 2 January 2015