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I will install Ubuntu on my machine on another HDD (an empty partition for Ubuntu). I will do this with Wubi to avoid having to burn a CD and is more practical at the moment. Is there any problem doing this?

With this approach, will I be unable to set the file system and partition for swap? Is there a problem installing this or not?

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There's a discussion on the pros and cons of Wubi on the Ubuntu forums. The downsides seem to be disk performance isn't as good as a regular installation, and there might be issues with standby/hibernation.

Regarding a partition for swap, you can create a swap file instead of a partition using this guide.

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