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ucberkeley / bce

Berkeley Common Environment provides a common Linux computational environment for classwork and research.
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RStudio-server installation script #58

Closed ck37 closed 8 years ago

ck37 commented 9 years ago

It would be nice if we provided a simple RStudio-server installation script. It's a very handy service that I think a lot of people may use, although maybe not worth auto-enabling by default.

The commands are essentially:

wget https://download2.rstudio.org/rstudio-server-0.99.467-amd64.deb
sudo gdebi rstudio-server-0.99.467-amd64.deb
sudo adduser rstudio

I will try to implement this sometime if someone doesn't beat me to it.

And in theory, we might be able to use instance meta-data (http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/ec2-instance-metadata.html) so that people can add a tag for "rstudio-server" when creating the instance so that the script runs without requiring an ssh and manual execution. Not sure how to implement that yet though.

cboettig commented 9 years ago

You can also take a look at the recipe we use in the rocker project: https://github.com/rocker-org/rocker/blob/master/rstudio/Dockerfile

Minor differences -- we query RStudio's data to look up which is the latest version, and we symlink the pandoc binaries installed by RStudio. We found having separate installations of pandoc in and outside of rstudio could lead to unexpected behavior due to version differences, etc when using rmarkdown functions in and out of RStudio. (also, I think adduser will prompt for info unless you include some other arguments? Note that you cannot just do useradd instead because RStudio server will fail to launch if it cannot find a home directory for the user. Of course using oski would probably sidestep these issues).

Also just thought I'd note that we had to get permission from RStudio to distribute their product packaged with other software in binary form (e.g. an image or container) to meet with their trademark rules. They were very nice and accommodating about this and maybe that's already been taken care of for BCE.

paciorek commented 9 years ago

Chris, if you do create the script, please link to it from http://bce.berkeley.edu/downloads.html, where there are some other add-on scripts to add functionality to BCE.

On Fri, Jul 24, 2015 at 10:42 AM, Carl Boettiger notifications@github.com wrote:

You can also take a look at the recipe we use in the rocker project: https://github.com/rocker-org/rocker/blob/master/rstudio/Dockerfile

Minor differences -- we query RStudio's data to look up which is the latest version, and we symlink the pandoc binaries installed by RStudio. We found having separate installations of pandoc in and outside of rstudio could lead to unexpected behavior due to version differences, etc when using rmarkdown functions in and out of RStudio. (also, I think adduser will prompt for info unless you include some other arguments? Note that you cannot just do useradd instead because RStudio server will fail to launch if it cannot find a home directory for the user. Of course using oski would probably sidestep these issues).

Also just thought I'd note that we had to get permission from RStudio to distribute their product packaged with other software in binary form (e.g. an image or container) to meet with their trademark rules. They were very nice and accommodating about this and maybe that's already been taken care of for BCE.

— Reply to this email directly or view it on GitHub https://github.com/ucberkeley/bce/issues/58#issuecomment-124594900.

aculich commented 8 years ago

@aculich will handle the non-technical issues @ryanlovett will handle the technical issues

cboettig commented 8 years ago

Just tested this on the Fall-2015 release and it is working rather nicely!

Perhaps you would consider adding /usr/lib/rstudio-server/bin/: into the PATH so it can be launched with just rserver?

ryanlovett commented 8 years ago

Technical issue fixed by 4546ff85ad116a02708fd174cda64e6af38cc904.

Ryan

On Tue, Oct 13, 2015 at 1:44 PM, Carl Boettiger notifications@github.com wrote:

Just tested this on the Fall-2015 release and it is working rather nicely!

Perhaps you would consider adding /usr/lib/rstudio-server/bin/: into the PATH so it can be launched with just rserver?

— Reply to this email directly or view it on GitHub https://github.com/ucberkeley/bce/issues/58#issuecomment-147847146.

paciorek commented 8 years ago

I'm trying this out now using fall-2015 and having an issue with having the rstudio-server processes launch. I think there should be an 'rserver' process running but it's not.

Any ideas?

ubuntu@ip-172-31-24-188:~$ sudo rstudio-server status ● rstudio-server.service - RStudio Server Loaded: loaded (/etc/systemd/system/rstudio-server.service; enabled; vendor preset: enabled) Active: active (running) since Thu 2016-04-14 21:50:51 UTC; 11s ago Process: 3066 ExecStop=/usr/bin/killall -TERM rserver (code=exited, status=0/SUCCESS) Process: 3081 ExecStart=/usr/lib/rstudio-server/bin/rserver (code=exited, status=0/SUCCESS) Main PID: 3082 (rserver) CGroup: /system.slice/rstudio-server.service └─3082 /usr/lib/rstudio-server/bin/rserver

Apr 14 21:50:51 ip-172-31-24-188 systemd[1]: Starting RStudio Server... Apr 14 21:50:51 ip-172-31-24-188 systemd[1]: Started RStudio Server. ubuntu@ip-172-31-24-188:~$ sudo rstudio-server verify-installation ubuntu@ip-172-31-24-188:~$ ps aux | grep rstudio rstudio+ 3158 0.4 0.6 192452 6884 ? Ssl 21:51 0:00 /usr/lib/rstudio-server/bin/rserver ubuntu 3180 0.0 0.2 8212 2108 pts/8 S+ 21:51 0:00 grep --color=auto rstudio ubuntu@ip-172-31-24-188:~$ sudo rstudio-server stop rsession: no process found

On Wed, Oct 14, 2015 at 1:28 PM, Ryan Lovett notifications@github.com wrote:

Technical issue fixed by 4546ff85ad116a02708fd174cda64e6af38cc904.

Ryan

On Tue, Oct 13, 2015 at 1:44 PM, Carl Boettiger notifications@github.com wrote:

Just tested this on the Fall-2015 release and it is working rather nicely!

Perhaps you would consider adding /usr/lib/rstudio-server/bin/: into the PATH so it can be launched with just rserver?

— Reply to this email directly or view it on GitHub https://github.com/ucberkeley/bce/issues/58#issuecomment-147847146.

— Reply to this email directly or view it on GitHub https://github.com/ucberkeley/bce/issues/58#issuecomment-148185742.

cboettig commented 8 years ago

@paciorek What you show looks good to me, though I haven't tested the BCE script recently. I believe the reason you're seeing rsession: no process found is because you haven't yet logged into the RStudio instance in the browser. (e.g. I get matching output to what you show above if I just use launch the rocker/rstudio docker image and exec into it. Once I log in through the browser, rstudio-server stop restarts the rsession instead of erroring with no process found

paciorek commented 8 years ago

Hmm, well, when I try to log on via the browser, the browser window immediately hangs and gives nothing back.

Also, I hadn't realized it until just now but it looks like rstudio-server is already installed in BCE-2015-fall. When I start a brand new instance and do not try to install the rstudio-server .deb and then check on the rstudio-server process status, things are as I previously described.

On Thu, Apr 14, 2016 at 3:07 PM, Carl Boettiger notifications@github.com wrote:

@paciorek https://github.com/paciorek What you show looks good to me, though I haven't tested the BCE script recently. I believe the reason you're seeing rsession: no process found is because you haven't yet logged into the RStudio instance in the browser. (e.g. I get matching output to what you show above if I just use launch the rocker/rstudio docker image and exec into it. Once I log in through the browser, rstudio-server stop restarts the rsession instead of erroring with no process found

— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/ucberkeley/bce/issues/58#issuecomment-210175298

paciorek commented 8 years ago

Never mind, I think it's just that I forgot to tell the instance to open the port.

On Thu, Apr 14, 2016 at 3:30 PM, Chris Paciorek paciorek@stat.berkeley.edu wrote:

Hmm, well, when I try to log on via the browser, the browser window immediately hangs and gives nothing back.

Also, I hadn't realized it until just now but it looks like rstudio-server is already installed in BCE-2015-fall. When I start a brand new instance and do not try to install the rstudio-server .deb and then check on the rstudio-server process status, things are as I previously described.

On Thu, Apr 14, 2016 at 3:07 PM, Carl Boettiger notifications@github.com wrote:

@paciorek https://github.com/paciorek What you show looks good to me, though I haven't tested the BCE script recently. I believe the reason you're seeing rsession: no process found is because you haven't yet logged into the RStudio instance in the browser. (e.g. I get matching output to what you show above if I just use launch the rocker/rstudio docker image and exec into it. Once I log in through the browser, rstudio-server stop restarts the rsession instead of erroring with no process found

— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/ucberkeley/bce/issues/58#issuecomment-210175298

paciorek commented 8 years ago

I believe we now provide rstudio-server.