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I want to install EtherPad on my Ubuntu Server.

The Etherpad installation instructions say:

Additionally, you'll need node.js installed, Ideally the latest stable version, be careful of installing nodejs from apt.

What does that mean? In my opinion, I can either choose to install it or not install it.

Do they mean that the version of nodejs distributed via apt may be an unstable or very old one?

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Short Answer

Just use the stable one from the repositories , it should be fine.

Long answer

The latest stable should hopefully end up in the repositories, as long as they are updated regularly.

The latest version currently is v0.10.25, which was released a week ago*, according to the nodejs website.
If nodejs is installed, dpkg can list the current version:

:~$ dpkg -l nodejs*
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name           Version      Architecture Description
ii  nodejs         0.10.15~dfsg i386         evented I/O for V8 javascript
ii  nodejs-dbg     0.10.15~dfsg i386         evented I/O for V8 javascript (de
ii  nodejs-dev     0.10.15~dfsg i386         evented I/O for V8 javascript (de
ii  nodejs-legacy  0.10.15~dfsg all          evented I/O for V8 javascript (le

So in Ubuntu 13.10, the latest version seems to be 0.10.15. According to the nodejs Changlog, this is the version from 2013.07.25 - the 25th July 2013, so it is half a year old*.

The EtherPad on GitHub shows that version 1.3, the latest version*, was released at the end of October 2013, so as this is only 3 months newer than the version of nodejs in the repositories, there us probably no need to bother.

Of course, if you wanted, you could download the latest stable version from here:

Though it would be easier to wait for the Ubuntu repositories to catch up Even though that can take a while...

*at the time of writing

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