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Is there any small VNC server program that can be set up using only command line?

I need this because my remote desktop server is not working (there is some license problem that I cannot solve right away.), and I only have access to server via SSH.

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Try X11vnc. It's easy to configure via the command prompt and it maintains the same session even if you close the vnc connection, so you can pick up later where you left off. It's in the Ubuntu repos, and likely in the repos for most distros. You can always compile it, if need be.

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Fedora has Tiger VNC Server.

The tigervnc-server-minimal package has everything to start it from the command line.

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What's the operating system of the remote server? If it's Windows (as the tags of your post suggest) you could use TightVNC. The current version comes as an MSI, but you can unpack that with e.g. 7-zip and rename tvnserverEXE to tvnserver.exe. tvnserver.exe -help will show you the commandline options.

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