Although it is also documented in the IBM Connections wiki here it is a short summary of the commands for Linux which might be useful. Although it describes the update to IBM COnnections CR1 it can be used for other fixes/fixpack as well:

IBM WebSphere and Lotus Buzz: IBM Connection update to CR1


If you are not logged in as "root" change to root access with just "su" and NOT "su -". And also be sure that you use the syntax ".  ./". If you do not precede the command with the period and space, the Java environment will not be properly set for the active shell.

IBM Connections update to CR1
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