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?
•
written
by
dark_rider_2010 •
Looks like you can install rstudio with conda. Theoretically (haven't tried) that should solve your issues with root permission and dependencies.
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.
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).
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.
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
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.
On the other hand, I don't have root access to install RStudio server version, and I couldn't find it in anaconda site.
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.
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.
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
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.
Yes you're right. It's a big server without nodes.
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.
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?
There is no problem, he just doesn't have time to solve my problems.
I think that is a pretty great advice to employ.
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
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.
If docker is available, you could try rocker's rstudio image and there are some instructions here.
Thanks, but it is not available.
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.
Log in to answer this question.
The easiest is probably to yell at your sysadmin or bribe with beer/chocolate.
@WouterDeCoster :)) Unfortunately our system admin is not kind at all and I can't use your advice.
if you have access to virtualbox, install small linux distributions (eg.DSL) and install rstudio and r in it.