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I am considering to use Ubuntu Server for a very low-end x86_64 machine. I am wondering what's the difference, and found this:

difference between ubuntu server, minimal, and desktop

I still have a question. My understanding is that minimal and desktop sort of share the software repository. All three share the kernels.

It seems that the set of software packages is different between server and the rest. My question is this: Are they configured and compiled differently?

I have been a Gentoo user. My understanding is, for example, Emacs can be compiled with and without X. Desktop Emacs packages seem to be built with X, which Server Emacs won't need. Does Ubuntu compile package--e.g. Emacs--differently? Or, does Ubuntu just drop Emacs for Server and ship it with X for desktop only?

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They all have the same repositories. The only difference is what packages get installed by default. Once you have an Ubuntu server up and running you can say tasksel install ubuntu-desktop and you get a fully-functional Ubuntu desktop. You could in principle start with Ubuntu desktop and then remove packages, but that would be a lot of useless work.

Some applications, such as Emacs and Vi, come in multiple variants, with or without GUI support. For Emacs, on a server with no graphics you would install the package emacs-nox.

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I don't know emacs; but a quick look at https://packages.ubuntu.com/disco/emacs (you didn't mention a release so I accepted default/latest) and it shows a dependency for emacs-gtk, thus if this was installed on a server without GUI it'd cause a load more packages to be installed to meet dependencies.

A search for emacs (https://packages.ubuntu.com/search?keywords=emacs&searchon=names&suite=disco&section=all) and I see

https://packages.ubuntu.com/disco/emacs-nox

which is the second install option (appropriate for a server without GUI).

The base of both server/desktop is the same, difference being only packages installed.

Both GUI and CLI emacs packages are available. You just select the most appropriate package for your system, and if you pick the wrong one you don't hit 'y' to install all the deps when you're asked to confirm.

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