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I have a live CD where are rkhunter and chkrootkit on. I like to run a Live CD and than check my hard disk (linux partition) with rkhunter and chkrootkit but I don't know how. When I mounted linux partiton and run rkhunter -c it check CD (live ) Linux...
Try chkrootkit's -r flag, and rkhunter's --rootdir flag. I have tried neither, but a quick perusals of their man pages (man rkhunter and man chkrootkit) and those look promising.
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