As Jkx wrote:

> This is really slow while writing (without any timeout msg).

Well, not a big surprise, with that slow ISP clock.

> And worst, the 32u2 has 32k vs 16k on the 162 of
> course.

Well, *that* was certainly expected, of course. :-)

>          SCK period      : 260.5 us

Try adding -B10 to the commandline.  That should make it substantially
faster.  I hope it will also cure the misreads.

> avrdude: Expected signature for AT90USB162 is 1E 94 82
> avrdude: safemode: lfuse reads as 5E
> avrdude: safemode: hfuse reads as D9
> avrdude: safemode: efuse reads as F4

ATmega32U2 has 1E 95 8A.  The signature read shows that the entire
read procedure is completely flakey.  At this point, you probably
shouldn't have used -F at all, to avoid additional failures resulting
from the poor communication.

-- 
cheers, J"org               .-.-.   --... ...--   -.. .  DL8DTL

http://www.sax.de/~joerg/                        NIC: JW11-RIPE
Never trust an operating system you don't have sources for. ;-)

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