Thanks for your additional information.
The logs should be fine, no more info needed. I was unable to reproduce
this problem on a i386 dapper->edgy upgrade but maybe I had a slightly
different set of eclispse packages installed.
** Changed in: gcj-4.1 (Ubuntu)
Status: Needs Info => Unconfirmed
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Update manager aborts on eclipse-platform-gcj when updating from Dapper to Edgy
https://launchpad.net/bugs/64395
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