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This is an additional document added to the Fedora RPM package of
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chkrootkit.
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-----
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It is in the nature of some of chkrootkit's checks that there may be some
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false positives among the reported findings. The chkrootkit user is
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advised to examine such files more closely (display them, query the RPM
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database about them, compare with backups on read-only media) and use
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another layer of protection (such as an intrusion detection tool).
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For example, where it is searched for hidden files below /usr/lib, which
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begin with a dot, chkrootkit may report files which belong into valid RPM
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packages, or which have been created at run-time by some software, and
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which are innocent. The output could look like this (the lines have been
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wrapped for readability):
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Searching for suspicious files and dirs, it may take a while... 
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/usr/lib/firefox-1.5.0.3/.autoreg
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/usr/lib/firefox-1.5.0.2/.autoreg
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/usr/lib/firefox-1.5.0.8/.autoreg
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/usr/lib/firefox-1.5.0.1/.autoreg
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/usr/lib/qt-3.3/etc/settings/.qt_plugins_3.3rc.lock
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/usr/lib/qt-3.3/etc/settings/.qtrc.lock
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/usr/lib/firefox-1.5/.autoreg
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/usr/lib/perl5/5.8.8/i386-linux-thread-multi/.packlist
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/usr/lib/firefox-1.5.0.4/.autoreg
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In this example, the files are valid files from Firefox (previous and
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current versions), Perl and the Qt GUI toolkit, but only the ".packlist"
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file is included in the main "perl" package. Creating and maintaining a
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simple white-list inside chkrootkit would bear the risk that a new rootkit
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uses the knowledge about white-listed file locations to store its
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malicious files.
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Also see:  http://www.chkrootkit.org/faq/