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suphp directory not owned by user
note that if you are letting other users put php into a directory, where it will be run as user tom, you are letting them run arbitrary commands as tom already
“tar: unrecognized option --warning” during 'apt-get install'
what version does "apt-cache policy x11-common" list for "Candidate". I ask because I suspect that you might be upgrading a debian 5 (currently "oldstable") server using sources pointing at debian 6 (currently "stable").