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installing new kernel broke my system

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http://www.linuxquestions.org – while recompiling the kernel I managed to screw up a bunch of my access permissions. Nothing is working right. The problem, is that I cannot find any sign of a problem, so I'm not even sure what to check. Bottom line, there were only three commands run as root before the problem occoured. Code: 1. sudo make modules-install 2. sudo make install 3. sudo shutdown -r now Has anyone ever seen the kernel install script screw up access permissions? I'm sorry about the vagueness of this question. Further details an be found in my first post which I have been having trouble getting anyone to respo (HowTos)