I am using Ubuntu 9.04, and have installed BOINC from the Ubuntu repository, version 6.2.18.
Is there an easy way to upgrade this to a newer version?

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One punch says a thousand words.

Yes. Completely uninstall it and go to http://boinc.berkeley.edu/download_all.php to get a newer version and install it to your HOME directory.

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That isn't really what I had in mind.
I don't really want to use the Berkeley installer, I like having BOINC installed via the Synaptic package management system.
What I wanted to know was, can I update my installation manually by replacing the BOINC binaries (boinc, boinccmd and boincmgr) with newer versions, and what other files would also need to be replaced?
If I upgraded like this would my BOINC work correctly?

I suppose the ideal solution would be if the version in the Ubuntu repository was upgraded to a later version. I wonder who is responsible for doing it, and why they haven't bothered about updating it?

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One punch says a thousand words.

Since you already have a version 6.x BOINC installed, it should work as you've planned (replacing the executables). Slight problems could arise if you are using CUDA devices to crunch.

Gruß,
Gundolf

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Computer sind nicht alles im Leben. (Kleiner Scherz)

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There is no newer BOINC client in the Ubuntu repositories. - The Ubuntu peoples are responsible to update BOINC in the repositories.

I recommend you, as the others has written, to update to the offical BOINC release.