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The Software Center didn't work and ask to check connection but my internet connection is working. Also, sometimes it says I have an a problem and asks me if I want to report it.

Anway, How could I install the Nintendo DS emulator.

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Which emulator? – Dominic Jordan Hasford Sep 26 '12 at 3:58
Check your sources.list for errors. – Rinzwind Sep 26 '12 at 5:18

Find out the exact name of the emulator (I could find only one called desmume) and install it by typing "sudo apt-get install name-of-the-emulator" in a terminal-window and hit [ENTER].

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Before installation do sudo apt-get update maybe emulator have new version in repo now, but you apt does not know about it. Old version files are not exist on server already and error occurs. By update sources list you apt will know new filename of package.

After update try install by sudo apt-get install youemulatorname and see messages.

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