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In my target eclipse, version 20020109++, selecting the "Open a type in the Editor" button in a "Hello World" workspace takes three minutes the first time. I had switched JRE's a few times before clicking the button and the dialog counted down (very slowly) from "Indexing 10 files"
You might simply be running out of memory if running 2 Eclipse IDEs at the same time... did you look at the memory usage (task manager) ? Switching JREs will cause some reindexing to occur, and prevent any search queries to succeed ('indexing 10 files' message), but indexing should be quick...
My system's memory is less than half used (271M out of 768M). 0 swap usage. I see this problem every time I switch JRE's and then try to open a type. Whatever it's doing, it's pounding my processor (1.3 GHz P4).
Note also that it seems particularly slow after switching to a Sun JDK.
*** This bug has been marked as a duplicate of 7616 ***