"Building new INDEX files..." takes more than 3 hours

I executed command
# portsnap extract
it goes well to the point where it prints
Code:
"Building new INDEX files..."

My problem is that it already stayed here for more than three hours utilizing 100% of CPU. This happens in Qemu and has the consequence that I am unable to connect TightVNC to virtual machine (it writes "Status: Connection established." but doesn't show screen).

My questions:
  1. is it OK that indexes are being built for three hours already?
  2. if it is wrong, then what to check?
  3. if it is normal, then what is the reason for such a huge time usage, can the algorithm be improved?
 
No, three hours is way too long. Even on a moderately old machine it shouldn't take that long.

Try removing the /usr/ports/INDEX file. And try portsnap again. If that fails again you can try building INDEX yourself with:
# make -C /usr/ports index
 
I created another virtual machine from backup. Then I removed # rm -rf /usr/ports/* on this new machine, and redeployed with # portsnap fetch extract successfully. On the new machine the index was built without hanging.

On the original machine the process is still not finished.
 
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