my R version on the zsh shell is the 3.6 that is different respect to the one of RStudio that is the 4. In fact, using the Jupyter notebook, the R version is the one used by conda. In fact, to install an r package I must run conda install -c r r-package_name. So, this is very annoying. How can I link the R version of Rscript of the shell with the one of the Rstudio?
Related
I have jupyter notebook installed, I also have R installed. Both work fine independently.
When I run jupyter with jupyter notebook, then try to open an ipynb file, I see
The only option in the dropdown is Python 3 (R is not an option).
Question
How do you open a jupyter notebook with an R kernel (on mac)?
Note
I tried jupyter notebook --runtime-dir /usr/local/bin/R but that was just guessing
Looks like the R kernel could be installed via pip?
Open any R session (e.g. in RStudio is fine, or open terminal/bash and type R to start an R session).
Install the kernel with:
install.packages("devtools")
devtools::install_github("IRkernel/IRkernel")
IRkernel::installspec()
Close and reopen the notebook and the R kernel will now be available.
If the R kernel does not appear as an option within a Jupyter notebook even after installing R, and one is using Anaconda, bringing up the conda prompt from the Start menu (Windows 10), and running the following commands may do the trick:
conda config --add channels r
conda install --yes r-irkernel
Credit to this post.
I have anaconda installed and use their version of jupyter notebook. I installed R
and IRKernel to make use of R in jupyter.
I can install packages on this version of R (3.5.1) and use them in jupyter.
I have installed a new version of R (3.5.2) using upgradeR() without problems.
To add this version to Jupyter I tried IRkernel::installspec(name = 'ir52', displayname = 'R 5.2') in R but this doesn't work.
I did this using R in jupyter notebook and this gave no errors and I can select the new kernel.
But when I select the R 5.2 kernel and do 'version' this gives the 5.1 kernel. What have I done wrong?
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
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.)
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
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:
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.
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.
Making a soft link works for me:
ln -s /opt/miniconda3/envs/r-4.2/bin/R /usr/bin/R
if is up to any good (now)... conda has the package rstudioapi which brings Rstudio to your local environment, and picks up the local/default r-base installed of your active environment.
you can install it (once your environment is activated) by typing:
conda install -c conda-forge r-rstudioapi
then you just type (inside your environment): rstudio
I have been using ipython notebook to run some R scripts. Now the problem is I have two R versions on my Ubuntu 14.04.
One is R.3.2.2 at /home/MYNAME/anaconda2/bin/R, another one is the R which I need for R studio,
now the problem is I want to only use R.3.3.1 for my system as I need some advanced task to be done.
I use conda uninstall r, after running this, according to the print out, a lot of R related packages is removed, if i run conda uninstall r again, it said
Fetching package metadata .......
Using Anaconda Cloud api site https://api.anaconda.org
Solving package specifications: ..........
Error: no packages found to remove from environment: /home/MyName/anaconda2
but when I run Which R again, still it is the anaconda R, if I run R in the terminal, it is still R3.2.2, anyone knows how could I remove this anaconda R version?
You probably needed to run hash -r in your session (or rehash if using zsh) to update your executables on PATH for the which command. A new terminal session would also fix the problem.
you can try conda uninstall r-base, this will remove R and all of the R-library.
The questions also implies that one cannot use anaconda R with rstudio.
On Linux you can
export RSTUDIO_WHICH_R=/home/USER/anaconda3/bin/R
and add to .profile (d/o your distro) to use rstudio with anaconda R and packages
I recently installed the Anaconda3 distribution and I want to have the R and Julia Kernels available besides Python. I use windows 10.
To install IJulia I installed the Julia language and follewed the steps indicated in the IJulia page; everything went fine.
To install the R kernel I used the command conda install -c r r-essentials in the anaconda command prompt, again, no problems. I also installed R.
When I launch the notebook the only available kernel is Python, the R and Julia kernels doesn't appear in the list, I have no clue why this since I got no errors in the installation of IJulia and IRKernel. Anyone could help?
After a fresh installation of Anaconda Distribution (either 2 or 3), following steps should be performed to achieve the desired kernels (R & Julia) on your notebook.
To install R on Anaconda(2/3) Jupyter Notebook :
Open 'Anaconda Command Prompt' & execute conda update notebook to update your Jupyter notebook to the most recent version.
Then install IRkernel by conda install -c r notebook r-irkernel
Now you may open R in your command prompt by running R.exe
Install all necessary R packages using the following lines in the R console by executing :
install.packages(c('repr', 'IRdisplay', 'evaluate', 'crayon', 'pbdZMQ',
'devtools', 'uuid', 'digest'))
devtools::install_github('IRkernel/IRkernel')
Finally, make the R kernel available to your Jupyter Notebook by executing:
Install only for the current user ➡ IRkernel::installspec()
For System-wide installation(all Users) ➡ IRkernel::installspec(user = FALSE)
To install Julia on Anaconda(2/3) Jupyter Notebook :
First, download Julia version 0.4 or later and run the installer. Then run the Julia application (double-click on it); the Julia Console with a julia> prompt will appear.
Now, for the most important step, open 'Anaconda Command Prompt' & execute where jupyter to see the actual path of your Jupyter Notebook. The output will be something like "C:\Users\JohnDoe\AppData\Local\Continuum\Anaconda3\bin\jupyter.exe"
Copy the above location and go to your Julia console. Now, execute the following respectively:
ENV["JUPYTER"]="C:\\Users\\JohnDoe\\AppData\\Local\\Continuum\\Anaconda3\\bin\\jupyter.exe"
Pkg.add("IJulia")
Pkg.build("IJulia") (Optional, execute if further error occurs again.)
⬆ Notice that the backslashes have to be doubled when you type them as a Julia string. I've just assumed that the path is your Anaconda path with \bin\jupyter appended, but replace that with whatever where jupyter tells you.
After few minutes, in Julia console execute:
using IJulia
notebook()
Now, you can program Julia in your Anaconda Jupyter Notebook.
Excellent, it worked.
However, it is important to import the package first before adding it.
import Pkg; Pkg.add("IJulia")