Question: Is there any way to install RStudio (or any other powerful IDE for R) without root access?
1
gravatar for dark_rider_2010
21 months ago by
dark_rider_201010 wrote:

We have a server and I have a user but not root access. The packages of R are installed on server but not RStudio. I tried to install RStudio but couldn't find any way, is there any way to install RStudio or any other IDE (which is as powerful as RStudio) on linux without root privileges?

R software error • 3.2k views
ADD COMMENTlink modified 9 months ago by ariel.balter140 • written 21 months ago by dark_rider_201010

The easiest is probably to yell at your sysadmin or bribe with beer/chocolate.

ADD REPLYlink modified 21 months ago • written 21 months ago by WouterDeCoster38k

@WouterDeCoster :)) Unfortunately our system admin is not kind at all and I can't use your advice.

ADD REPLYlink written 21 months ago by dark_rider_201010

if you have access to virtualbox, install small linux distributions (eg.DSL) and install rstudio and r in it.

ADD REPLYlink written 21 months ago by cpad011211k
5
gravatar for WouterDeCoster
21 months ago by
Belgium
WouterDeCoster38k wrote:

Looks like you can install rstudio with conda. Theoretically (haven't tried) that should solve your issues with root permission and dependencies.

ADD COMMENTlink written 21 months ago by WouterDeCoster38k

conda installation is possible but not sure if its already there in their HPC else the OP needs to install conda in his/her home of the HPC since am sure there will be again a root access problem for conda installation.

ADD REPLYlink written 21 months ago by ivivek_ngs4.8k
2

since am sure there will be again a root access problem for conda installation.

No, I have anaconda conda installed as a regular user without root access and I can install everything I want (which is available through conda).

ADD REPLYlink written 21 months ago by WouterDeCoster38k

That's amazing idea. I installed anaconda and also installed Rstudio with it. But Rstudio has problem with vnc and nothing is working in it. Thanks again for your help.

ADD REPLYlink written 21 months ago by dark_rider_201010

Probably this issue will be solved with R studio server version. However take a look at the 2 below link. Probably you have to set the environment variable properly in your bash_profile. Take a look

Link1

ADD REPLYlink written 21 months ago by ivivek_ngs4.8k

I can run RStudio, but I/O is not working in it. I searched about it, and it is a bug that rstudio is not compatible with vnc (which is used to work with server). Thanks a lot.

ADD REPLYlink written 21 months ago by dark_rider_201010

On the other hand, I don't have root access to install RStudio server version, and I couldn't find it in anaconda site.

ADD REPLYlink written 21 months ago by dark_rider_201010

Rstudio has problem with vnc

What kind of problem? Not able to get the GUI to display?

ADD REPLYlink written 21 months ago by genomax65k

I can run RStudio, but nothing is worked in it (keyboard), when I drag mouse, something bad happens and rstudio crashed. I searched the problem and maybe it is a bug and rstudio is not compatible with vnc.

ADD REPLYlink written 21 months ago by dark_rider_201010
1

Instead of using vnc I suggest that you try an SSH program (PuTTy should work or SSH secure shell client, use this version since it was the last free version available) and a X-windows application for displaying tunneled X11 data on your local machine.

ADD REPLYlink written 21 months ago by genomax65k
2
gravatar for Sergey Naumenko
21 months ago by
Sergey Naumenko350 wrote:

Hi dark_rider_2010!

Have you tried, instead of trying to hack the system, to understand your sysadmin? Even if you install R-studio, which is possible, your sysadmin will figure it out very soon, and ... will get angry.

When I was an angry sysadmin, I was definitely against the installation of R-studio neither on the main node of HPC, nor on the computing nodes. On the main node - because RStudio users may hang this node soon creating a mess for other users, and may destroy some critical services at the same time. On the computing nodes - because they don't have GUI libraries, and they have to have a standard package set.

Once I had several people who wanted to run R-Studio on HPC, I with my fellow angry sysadmin installed R-Studio server on a dedicated node, which we excluded from the job queue, and people started working via the web interface.

Why do you need R-studio on HPC at all? You can run it on your laptop mounting your HPC as a folder via SSHFs to debug your scripts using small subsamples of real data. Once you are done with debugging, you can run your scripts on HPC in R without R studio.

Good luck

Sergey

ADD COMMENTlink written 21 months ago by Sergey Naumenko350

It might be just a big server without an architecture with computing nodes and main nodes, but for the remainder I think that's excellent advice here.

ADD REPLYlink written 21 months ago by WouterDeCoster38k

Yes you're right. It's a big server without nodes.

ADD REPLYlink written 21 months ago by dark_rider_201010

Oh, no you got it wrong. Our admin just doesn't have time to install RStudio and doesn't have any problem with installing it and I am not hacking the system of course! I need to run a machine learning algorithm and see the results step by step and that's why I need an IDE.

ADD REPLYlink written 21 months ago by dark_rider_201010

Then, in that case, raise a ticket with proper information to your sysadmin and see what their response is. If there is no computing nodes and architecture I do not see any problems in installation. How are other bioinformatics researchers dealing with this?

ADD REPLYlink written 21 months ago by ivivek_ngs4.8k

There is no problem, he just doesn't have time to solve my problems.

ADD REPLYlink written 21 months ago by dark_rider_201010

I think that is a pretty great advice to employ.

ADD REPLYlink written 21 months ago by ivivek_ngs4.8k
1
gravatar for Santosh Anand
21 months ago by
Santosh Anand4.7k
Santosh Anand4.7k wrote:

Like many other linux-packages, RStudio can be installed from source in a preferred directory by giving this option at configuration

CMAKE_INSTALL_PREFIX=/your/fav/dir

see https://github.com/rstudio/rstudio/blob/master/INSTALL

ADD COMMENTlink written 21 months ago by Santosh Anand4.7k

Thanks, I tried this, but there are lots of dependencies and they need root access for installation. I read ReadMe file and the steps need root privileges.

ADD REPLYlink written 21 months ago by dark_rider_201010
1
gravatar for Jean-Karim Heriche
21 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

If docker is available, you could try rocker's rstudio image and there are some instructions here.

ADD COMMENTlink written 21 months ago by Jean-Karim Heriche18k

Thanks, but it is not available.

ADD REPLYlink written 21 months ago by dark_rider_201010
0
gravatar for ariel.balter
9 months ago by
ariel.balter140
ariel.balter140 wrote:

You can easily install both rstudio and spyder with conda without root access.

You should also consider using Jupyter notebooks. You can install jupyter with conda as well.

Caveats:

1) You need to install all the R packages and python packages you want to use. 2) If you are going to use conda, eliminate all the path variables for R and Python you have set. You need to let conda handle them. In other words: conda do yes--ok, conda do no--ok, conda do "guess so"--squish like grape.

ADD COMMENTlink written 9 months ago by ariel.balter140
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