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/usr/share/doc/pbnj/NOTES-ON-NMAP-VERSION is in pbnj 2.04-4.

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The version of Nmap you have installed will affect the
performance of PBNJ 2.0. If you are running a version older than 
Nmap-4.20ALPHA3, then Nmap won't be able to properly identify the OS 
when no services are running. Thus, if you scan a machine that is 
running services, then scan it when all the services are off, 
PBNJ 2.0 will consider the operating system to different as the OS 
for the 2nd scan is unknown. This is because there is nothing for 
Nmap to connect to, so Nmap is not able to return a proper 
fingerprint. Therefore, this would cause the machine from scan 1 to 
show all services as still running and the machine from the 2nd scan 
to be inserted as a new machine with no running services.