How to set up conda-installed R for use with RStudio?
Solution 1
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
Solution 2
See https://anaconda.org/r/rstudio:
$ conda install -c r rstudio
Then from command line:
$ rstudio
(It is how I installed it and it works.)
Solution 3
Update: ADD THIS TO ~/.bash_profile
!
export RSTUDIO_WHICH_R="/Users/jespinoz/anaconda/bin/R"
launchctl setenv RSTUDIO_WHICH_R $RSTUDIO_WHICH_R
Credits to @Z-Shiyi for the last line https://github.com/conda/conda/issues/3316#issuecomment-241246755
An addition to what @Ray Donnelly said above. Basically, it has to be executed from the correct environment (i.e. run it from the terminal).
You can either:
(A) Put this in your ~/.bash_profile
export RSTUDIO_WHICH_R=/Users/[yourusername]/anaconda/bin/R
(if youre using conda but you could put any R
path)
(B) then type this in the terminal after it's been sourced (either restart terminal or do source .bash_profile
): open -a RStudio
That should work.
or you can do what I did:
(A) open up automator (sorry if you're not on a mac; this will only work on mac)
(B) use a Run Shell Script
(C) then delete cat
that's already in there and put in:
export RSTUDIO_WHICH_R=/Users/[yourusername]/anaconda/bin/R
open -a RStudio
(D) Save it as something like run_rstudio.app
then just run that and it should work:
Solution 4
Launch RStudio from Activated Conda Environment
At least for Mac OS X, I find that it is sufficient to activate the environment in a shell session, then launch RStudio.
$ conda activate my_r_env
$ /Applications/RStudio.app/Contents/MacOS/RStudio
Once in R, one can verify that values of R.home()
and .libPaths()
point to the environment-specific locations.
The advantage here is that you aren't fixed to whatever was last set in the environment variables, e.g., via .bash_profile
. Instead, one can have many R-based environments and switch between them (or run multiple ones simultaneously) without tampering with global settings.
Suggested Alias for Convenience
Perhaps the only global setting I might recommend is to add an alias for rstudio
to your .bash_profile
so you don't have to type the full path every time, like
alias rstudio='/Applications/RStudio.app/Contents/MacOS/RStudio &'
which enables one to then do
$ conda activate my_r_env
$ rstudio
$
where the &
enables one to continue using the shell, or close it, without affecting the RStudio instance.
Solution 5
Update: The Anaconda Distribution now has packages for RStudio so you should be able to use that and not have to jump through any hoops at all. You can also install it directly the Anaconda Navigator.
O.rka
I am an academic researcher studying machine-learning and microorganisms
Updated on September 02, 2021Comments
-
O.rka over 2 years
I've been trying to set up my
R
usingconda
(eventually to use with Beaker Notebook) and I want to be able to useRStudio
with my conda-installed version ofR
.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
inJupyter
is kind of buggy. For example, when it outputs errors, it outputs tostdout
and splits every character in the string with a linebreak. I want to useRStudio
but I don't want to install another version ofR
.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 (Isourced
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 -
O.rka over 7 yearsHow can I make sure
rstudio
is launching from that same environemnt? -
O.rka about 7 yearsI recently saw this when I opened up
anaconda navigator
for the first time. I added my solution above. It has been working perfectly so far. -
O.rka about 7 yearsIn hindsight, I should have done that. I don't think this was an option for when I first tried it. At least we have at least 3 different ways to get this to work for people :)
-
Ray Donnelly about 7 yearsSince the latest 4.3 release of Anaconda Distribution, none of this should be necessary. Installing and launching RStudio from Anaconda Navigator should 'just work' and, from Terminal, provided you activate your env properly (conda.io/docs/using/envs.html)
open $CONDA_PREFIX/Applications/RStudio.app
should also work. -
empty over 6 yearsOn Windows 10 and Anaconda3 it's simply
conda install rstudio
-
gsmafra almost 6 yearsCan't I use the conda R interpreter with a default RStudio installation (downloaded from RStudio website)?
-
Belter about 5 years
$ rstudio &
, run as a deamon process -
fry almost 4 yearsIf you wish to have only one version of Rstudio (with your settings), but interact with different conda environments, this is the perfect solution (cannot attest to whether that works with other operating systems).
-
Georg Heiler over 3 yearsBUT: rstudio in conda is not updated. It seems to be rather outdated i.e. 1.1 on osx vs. now 1.4 available.
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merv almost 3 yearsUpdate: Anaconda abandoned maintaining RStudio builds for Conda, and while Conda Forge is discussing picking it up, there's no momentum. This might change, however, once RStudio transitions from Qt to Electron (supposed to drop this summer), since it should simplify the build. Anyway, point is Conda does not reliably provide RStudio builds.
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william_grisaitis almost 3 yearsdown-voting for the headline, which is (1) outdated for anyone running macOS 11+ (a lot of ppl) and (2) kind of obnoxious
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Naeem Khoshnevis almost 3 yearsWorks great with macOS.
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merv over 2 yearsOutdated answer. As mentioned by others, RStudio from Conda is not maintained and will only work with at most R 3.6.