Issue
I've been trying to set up my R
using conda
(eventually to use with Beaker Notebook) and I want to be able to use RStudio
with my conda-installed version of R
.
My method of installing R
:
conda install -c r r
conda install -c r r-essentials
conda install -c r r-rserve
conda install -c r r-devtools
conda install -c r r-rcurl
conda install -c r r-RJSONIO
conda install -c r r-jpeg
conda install -c r r-png
conda install -c r r-roxygen2
conda install --channel https://conda.anaconda.org/bioconda bioconductor-edger
I ran that version of R (I only installed this version)
> version
_
platform x86_64-apple-darwin11.0.0
arch x86_64
os darwin11.0.0
system x86_64, darwin11.0.0
status
major 3
minor 3.1
year 2016
month 06
day 21
svn rev 70800
language R
version.string R version 3.3.1 (2016-06-21)
nickname Bug in Your Hair
Running R
in Jupyter
is kind of buggy. For example, when it outputs errors, it outputs to stdout
and splits every character in the string with a linebreak. I want to use RStudio
but I don't want to install another version of R
.
How can I route my conda version of R
into RStudio?
Here's my .bash_profile
not sure if this will be useful:
$ cat ~/.bash_profile
# added by Anaconda3 4.0.0 installer
export PATH="/Users/jespinoz/anaconda/bin:$PATH"
export RSTUDIO_WHICH_R=/Users/jespinoz/anaconda/bin/R
I've been trying to follow these tutorials but I am lost. I'm really not too familiar with environment variables and such things.
(1) https://support.rstudio.com/hc/en-us/community/posts/207830688-Using-RStudio-with-conda
(2) Launch mac eclipse with environment variables set
when I looked for my R
it directed me to:
$ which R
/Users/jespinoz/anaconda/bin/R
but the directions from (1) is using this path which is very confusing:
/Users/jespinoz/anaconda/lib/R/bin/R
I tried doing what this guy did and added this to my .bash_profile
but it didn't work. I even made a .bashrc
but it still didn't work (I sourced
both after I added the lines)
export RSTUDIO_WHICH_R=/Users/jespinoz/anaconda/bin/R
How to tell RStudio to use R version from Anaconda
Unfortunately, anaconda
has no tutorial for this in https://docs.continuum.io/anaconda/ide_integration
Solution
So long as which R
shows up a working R interpreter (which it should do if you have installed the r
package from conda
and activated your environment) then launching rstudio
from that same environment should pick it up just fine.
For a test, on ArchLinux
, I built and installed: https://aur.archlinux.org/packages/rstudio-desktop-git/
.. then force removed the R interpreter (pacman -Rdd r
), then installed r
from conda
(conda install -c r r
) and it worked fine. I then closed my terminal and opened a new one (so that the correct conda
environment was not activated and successfully launched RStudio with the following command: RSTUDIO_WHICH_R=/home/ray/r_3_3_1-x64-3.5/bin/R rstudio
I think the crux is to launch RStudio
from the right environment? Your ~/.bash_profile
and ~/.bashrc
are only sourced when you run bash
. For environment variables to be set so that the your desktop environment knows about them, on Linux, you should put them in ~/.profile
or else in /etc/pam.d
(you may need to logout or shutdown after making those changes) and on OS X, you should check out https://apple.stackexchange.com/q/57385
Answered By - Ray Donnelly Answer Checked By - David Marino (PHPFixing Volunteer)
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