Since the repositories are not updated often, it is best to manually download and install the updated versions of Plex Media Server manually. You may be forced to do this if you’ve seen the “An update is available. Please install the update manually.” error:

This is fairly simple (performed on Ubuntu 14.04):

1. Backup: Consider backing up your metadata and preferences.  Updating this package should not affect either, but better safe than sorry.  Plex wiki on what to back up.
2. Grab the file and get it to the server: Now you need to get the new package onto the server. You can do one of two things:
   Transfer using WinScp: Go to the Plex Media Server download site, log in, and download the latest version (be sure to check under “PlexPass”), then manually move it onto the server using a program like WinSCP.
   OR…
   Directly download the file to the server: Figure out the URL for the file to be downloaded, and then just use wget on the Linux server (this is just an example URL – find the current version!):

   plexuser@plexserver:~$ wget https://downloads.plex.tv/plex-media-server/0.9.11.7.803-87d0708/plexmediaserver_0.9.11.7.803-87d0708_amd64.deb

3. Install: Pretty easy! Just install the .deb file:
   

   plexuser@plexserver:~$ sudo dpkg -i plexmediaserver_0.9.11.7.803-87d0708_amd64.deb

   You’ll get something that looks like this:

   plexuser@plexserver:~$ sudo dpkg -i plexmediaserver_0.9.11.7.803-87d0708_amd64.deb
[sudo] password for plexuser:
(Reading database ... 198842 files and directories currently installed.)
Preparing to unpack plexmediaserver_0.9.11.7.803-87d0708_amd64.deb ...
plexmediaserver stop/waiting
Unpacking plexmediaserver (0.9.11.7.803-87d0708) over (0.9.11.5.774-760cb52) ...
Setting up plexmediaserver (0.9.11.7.803-87d0708) ...
plexmediaserver start/running, process 8686
Processing triggers for bamfdaemon (0.5.1+14.10.20140925-0ubuntu1) ...
Rebuilding /usr/share/applications/bamf-2.index...
Processing triggers for desktop-file-utils (0.22-1ubuntu2) ...
Processing triggers for mime-support (3.55ubuntu1) ...
Processing triggers for gnome-menus (3.10.1-0ubuntu2) ...
Processing triggers for ureadahead (0.100.0-16) ...
plexuser@plexserver:~$


4. Verify: That’s really all there is to it. The command above should have restarted your server automatically for you. On your Plex server web panel, navigate to: Settings->Server to verify that you’re on the latest version!