Safari 3.2.x freezes computer, solved, RSS Database was corrupted.

Question

*Short answer:*
rm ~/Library/Syndication/Database3
rm -rf ~/Library/Caches/com.apple.Safari
*Long answer*
Ever since I "upgraded" to Safari 3.2 it would freeze my iMac G5. Even after "upgrading" to 3.2.1 the problem persisted. However, this problem did/does not occur on my iBook G4.
First off, I switched to Firefox 3. So kudos to Apple for giving me the opportunity to ditch Safari. I've been a daily user since 2004 but "it just works" was more important to my productivity than having my computer freeze for no immediately obvious reason. Next up, ditching OS X for Linux? Haha, just kidding. Maybe.
Still, I need to debug websites in Safari. And up until an hour ago, Safari would freeze my computer.
Yes, I read all the threads about how to fix the problem(s). Yes, I cleared my preferences files. Yes, I repaired disk permissions. And no, I don't run any input managers or third party hacks.
What I did find out, after patiently waiting and letting a few log messages painfully trickle into the console, was that ~/Library/Syndication/Database3 was corrupted.
Console:
[phone]:37:06.949 Safari[1001] WARNING: SQLite error 10: disk I/O error+
[phone]:37:06.950 Safari[1001] WARNING: SQLite error 10: disk I/O error+
[phone]:37:06.950 Safari[1001] WARNING: SQL query failed:+
+SELECT source_id,COUNT(id) FROM Articles WHERE unread=1 GROUP BY source_id+
System:
+Nov 30 18:37:07 iMac kernel[0]: disk0s3: I/O timeout.+
Database3 is where Safari keeps it's RSS feeds. Database3 is a Sqlite database. The new "Fraudulent websites" as well as the new "Database Storage HTML 5" features are also Sqlite based. My guess is that a botched upgrade messed something up. Either that, or the file was on a bad sector. However, because Safari kept locking my system (and making me curse very loudly in the process) I ran disk repair several times last week, at bootup, off the Tiger install CD, to no avail.
The solution, for me, was to delete the ~/Library/Syndication/Database3 file.
In the process of being ticked off, i deleted the ~/Library/Caches/com.apple.Safari cache directories for good measure. Why? Because that's where you will find SafeBrowsing.db, an sqlite database used by the Fraudulent websites feature.
Everything is back to normal, at least for now... Thanks for reading.
PS: For those who want to mess around with the sqlite database files but are afraid of the command prompt, check out: http://sqlitebrowser.sourceforge.net/

Answer 1

For your own sanity's sake and future sake of your system, you should run a disk block check using Apple Hardware Test, TechTool Deluxe or Pro, or DiskWarrior, whichever you have available.
The disk I/O error is a real phenomenon - there was a disk error reading a block on the disk.
By deleting the file in question, the bad block was released back into the free disk block pool, meaning it will show up in some other file in the future if it's actually a physical bad block on the disk.
What's more likely is that it was a block written with a bad checksum, which means the bad block will correct itself the next time that block on the disk is written to, so you may not see it again even if you use one of the disk tools I mentioned above.
But it's always good to test to make sure it isn't a physical bad block that will come back to haunt you when some other file on your system uses that disk block.