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"sudo apt-get install rJava" on Ubuntu 12.04 (precise pangolin) does not install the current version

You can't have your cake and eat it: If you use Ubuntu 12.04, you are effectively saying that you value stability first, and so you are using a 2 1/2 year old distro. And you get the packages contained in that version.

Now, if you were to run Ubuntu 14.04, you would be getting 0.9-6. Just like that. And 14.04 is also an LTS release, so I'd upgrade.

Lastly, you have 3.1.0 (not 3.10 as wrote as the latter does not exist) so somehow you must have managed to figure out how to add other repos. So with that, maybe re-read the fine README by Michael at CRAN as I believe that one of his additional repos may well have a newer rJava backported to 12.04.

Ultimately the problem of trying to mix a newer R (which you installed) with an older distro release (which you still use) is of your making: the R in 12.04 will run with the rJava in 12.04.

So I would just upgrade. Lots of other software got better too.

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