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I'm a relatively new user of Ubuntu, version 8.04. I recently had a system glitch that disabled my $HOME/.dmrc directory. I managed to get my home directory back under my ownership with 644 privileges, and went on about my business. Then a couple of days later (today) I noticed that a website that required Java wasn't running right.
I checked Firefox's preferences and "Enable Java" is checked. My Java Runtime Environment is installed - and it was working a week or so ago when I visited this same website. However I went back to my firefox and java directories (the former is in my /usr/lib directory and the latter in my home directory) and noticed that the ownership of the directories is different: $HOME/java is owned by me (as it should be since I changed the ownership of my home directory back to myself recently), but /usr/lib/firefox-3.0.4 is owned by root.
The normal process of enabling Java involved placing a link to my JRE (in $HOME/java) in my firefox folder. Did changing ownership of that $HOME/java folder while leaving my firefox folder with root break that link?
Distribution: Ubuntu 10.04 (used to be Red Hat 7.1, then Red Hat 9, then FC 2, FC 5, FC 6, FC 9 and Ubuntu 8.04)
Did you perhaps set 644 privileges on subdirectories in your home directory? If you do ls -la you should see directories with drwx------ or drwxr-xr-x i.e. "executable" permission should be enabled on directories. If you see them as drw-r--r-- then you must have applied your 644 setting to directories - if so then just give the directories the x permission.