I've searched the web, and I'm still unclear on how to run R from the Mac terminal. I have Rstudio and the standalone R app installed. I thought I could just type "R" from the command line as I do with "python", but that doesn't work. Is it necessary to edit the PATH in my bash profile? If so, how do I give the correct location of R?
Thanks for any help
Edits after receiving comments
So, I'm running Sierra, and when I type "r" or "R" at the terminal, I get "-bash: R: command not found." If I type, "which R" in the terminal I do not get any output.
Here is the output from "echo $PATH": /usr/local/heroku/bin:/opt/local/bin:/opt/local/sbin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Users/samuelcolon/anaconda/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/Users/samuelcolon/.rvm/gems/ruby-2.1.0/bin:/Users/samuelcolon/.rvm/gems/ruby-2.1.0#global/bin:/Users/samuelcolon/.rvm/rubies/ruby-2.1.0/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/samuelcolon/.rvm/bin:/Users/samuelcolon/.rvm/bin
As for the installation, I believe I downloaded it directly from cran.r-project.org a while ago. I can locate the GUI in my applications and open it--
I have version 3.13. Is it possible, I only have R.app installed but not R? Perhaps that's the reason I'm getting the 'command not found' when typing "R" into the terminal?
Generally, I've been working in RStudio, but I'd still like to access R from the terminal and also to find where things are located. I'm fine with removing and re-installing R if it's easiest to start from square one. I hope the extra detail helps, and I appreciate the responses.
An answer for those not that familiar with Terminal and Bash.
I have done a fresh update install of R from the R.org cran site as part of seeking an answer to your question.
I found this latest install version 3.4.0 installs R for access in Terminal, and also installs R.app as part of the package.
To my understanding, reading support docs, if you have an older version of R it will update that. However it will not update an installation of R installed by the anaconda package.
Where are the R files stored?
I can only assume that with a fresh install of the latest R, R will work for you in Terminal.
To learn where the R files are that are being accessed - in Terminal after starting R, and in R.app, type:
>R.home()
In my case as example:
In R.app - the R version 3.4.0 is accessed in the top directory (not my user folder):
R.home()
[1] "/Library/Frameworks/R.framework/Resources"
In Terminal - the R version 3.3.2 is accessed in the Anaconda package, again in the top level directory.
R.home()
[1] "/anaconda/lib/R"
So I have two different versions of R, and Terminal accesses a different version to R.app.
How can I ensure I access the same version in Terminal as I do in the R.app?
For someone familiar with bash, and how the whole bash command system works I am sure there is a well constructed command. All the same here are some novice solutions.
-
• First Solution:
I could update the anaconda version, however, I would prefer not to as as other elements of the anaconda package my depend on this older version of R. For those not yet familiar with Terminal and bash, not such a novice solution.
-
• Second Solution:
This solution came from mko. It provides a single use solution. From the result above, and checking the directory structure a little further to find this R file.
Finding the significant R file enables me to edit an extension of the above path shown in the R.app. So add /bin/R to enter
/Library/Frameworks/R.framework/Resources/bin/R
Entering and pressing return will start R from this version.
Alternatively, one can find this file and icon in the GUI Finder, lead by the above result, and just double click on it, and it will open Terminal and a session with R running for you. Easy!
One could also make an alias of it and put it on your desktop for easy future starts.
-
• Third Solution:
My last solution I think may be best, adding to mko's solution. Make an alias.
Being in my home directory in Terminal I open .bash_profile using the nano text editor. (If you do not already know how to do this, then best not use this solution.)
I then add the line in this env file.
alias Rv340='/Library/Frameworks/R.framework/Resources/bin/R'
I then save the changes and exit this terminal session. I then open a new Terminal window. (This is so the changes to the env above are incorporated in the new terminal session).
Then when I enter the alias:
Rv340
The version of R I want opens.
You can choose a different alias name to "Rv340".
-
• Fourth Solution:
A second more permanent solution for opening the same version of R in Terminal is as follows.
Copy the path as showing in R.app in response to the R.home() command above, and add that path to PATH in your .bash_profile. (If you do not know already how to do this, then ignore this solution.) Do so as follows.
export PATH="/Library/Frameworks/R.framework/Resources:$PATH"
To my understanding, this ensures that bash looks here for R (and anything else), then moves on to the other paths in PATH. Since this adds this path to the beginning of $PATH, an env variable, bash looks here first where it finds the newer version first, and stops looking.
When it comes to understanding PATH in the env set up in .bash_profile the following two links were helpful.
About PATH.
How to correctly add a path to PATH.
This solution may muck with anaconda's invocation of R. I have yet to check this.
First of all, you have to start terminal application. You can use either built in Terminal.app, or you can use replacement. My favorite one is iTerm2
https://www.iterm2.com
Then, you simply open terminal window and run R. Just like shown below:
Have fun with R!
Just ran into the same issue when installing R-4.0.3.pkg on my MacBook (MacOS BigSur). Can open R.app to the clunky R GUI, but typing in 'R' in terminal doesn't work.
Turns out, an R executable lives here: /Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R
So I added this alias to my newly created .zshrc script:
alias R '/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R'
Now when I type in R, it opens... I swear this all happened seamlessly in earlier versions.
There is currently a bug in CRAN's R installation package that results in it not correctly installing symbolic links to R and Rscript for commandline use. I've just verified this by inspecting the postflight script in their 4.0.5 installation package. This only impacts MacOS system releases of 20 and above (you can check with uname -r).
I've included more info here, along with what the "correct" fix should be: manually creating symbolic links to /usr/local/bin that point to the R and Rscript binaries themselves. If this is the current challenge, then this would be a far better solution to creating aliases or manipulating PATH in various ways, since it's what the installation package intended to do (and presumably will again soon).
R: command not found
In short, if this is the problem, then Ashkan Mirzaee's answer (https://stackoverflow.com/a/67202173/2093929) to create the symbolic links directly is correct in form, but might not have the right link command. The 4.0.5 package intends instead to use:
mkdir -p /usr/local/bin
cd /usr/local/bin
rm -f R Rscript
ln -s /Library/Frameworks/R.framework/Resources/bin/R .
ln -s /Library/Frameworks/R.framework/Resources/bin/Rscript .
You can create a symbolic link from R and Rscript binaries to /usr/local/bin to add them to the PATH:
sudo ln -s /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R /usr/local/bin
sudo ln -s /Library/Frameworks/R.framework/Versions/Current/Resources/bin/Rscript /usr/local/bin
Now which R should return /usr/local/bin/R and you can use R.
An easy way to open RStudio with admin privilege on macOS:
Go to Applications, then right click on RStudio
Select "Show Package Contents"
Go to Contents/MacOS
Now open terminal(in bash mode). Type sudo and drag the RStudio.exec into terminal and press on ENTER
Now RStudio will have admin access!
Related
enter image description here
Even I export the R path to be the correct one, rstudio still use the deleted R path.
I checked my ~/.bashrc file and the deleted path is not in $PATH variable...
Ok , thanks for user 42's answer.
However, I can't find where is .Rprofile located and I've made too many changes to configuration files that it's hard to pinpoint where's the problem any more. I completely erase my disk division and reinstall ubuntu.
My system is ubuntu server so I try to install everything just as user rather than root. And specifically I install R, R-essentials using conda in the directory /usr. This time the Rstudio can find R without problem. Therefore I think Rstudio can only find R in certain directories... like /bin /usr/bin. And somehow it ignores R in other directories.
I'm exploring package building on Windows 7 but have been running into trouble after reaching the Command Prompt stage. The following thread appears to be on the same topic that I'm having trouble with, but the question remains unresolved:
Cannot install R package in Windows 7
The problem: whenever I try an R CMD command in Command Prompt (e.g. I've tried R CMD install pkgName, R cmd install pkgName, Rcmd install pkgName, where pkgName is a place-holder for an actual package that has been R CMD checked on OS X and also posted on CRAN, where I have the unzipped source in the current working directory), I get the following error message:
'R' is not recognized as an internal or external command,
operable program or batch file.
(If I try the Rcmd install pkgName command, then the error starts out as 'Rcmd' is not ....) Note that even if I type in just R in Command Prompt and hit enter, I get the same error, so I'm not even able to bring up R here, though it opens perfectly fine in its stand-alone interface.
I have examined the following guides without success in identifying the trouble:
Karl W Broman's website
Rob J Hyndman's website
Steven Mosher's blog
The most immediate thing that came to mind was that the path variables in Windows were not set right, but this also has not (yet) led to the answer. For example, I have triple-checked the paths to ensure they are correct, including for the R version number, that x64 in the path name is accurate, etc.
I realize this is a complex issue to remotely diagnose, but any advice and suggestions on resolving this trouble is appreciated. For reference, below are the steps I have taken already to try to resolve this issue:
Uninstall R and Rtools
Install the latest version of R (2.15.0)
Install Rtools215 to match R version 2.15.0
Originally I let Rtools specify the path variables (turning that option on during installation). No success after this method.
I updated the path variables on my computer, where the below paths were used:
C:\Rtools\bin; C:\Program Files\R\R-2.15.0\bin\x64;
I've also tried the R CMD (and Rcmd) commands with the following paths included (note that these paths don't lead to anything on my computer, so I tried doing R CMD / Rcmd with and without them specified):
C:\Rtools\perl\bin; C:\Rtools\MinGW\bin;
Tried adding/removing the following path, which goes to the only other folder visible within the Rtools folder:
C:\Rtools\gcc-4.6.3;
Tried multiple variations of the R CMD commands, as noted earlier.
I tried this all a few months ago when I had R version 2.14.1 and Rtools214 installed, and I had the exact same trouble.
Note: I already had Cygwin installed prior to R and Rtools, and I have not installed MikTeX (yet).
Have you closed the command prompt and opened a new one after adjusting the PATH?
Enter the command PATH on the command line and ensure that you are properly updating your path
Try navigating to the directory where R.exe is saved and running it locally -- cd C:\Program...\bin\x64, R.exe.
Ensure that you're running on Windows' Command Prompt and not Cygwin's terminal
If you actually have a space after the semi-colon in your PATH, you'll need to remove that: /bin;C:/Program.... Try combining that with Joshua's solution.
I attach my whole solution here:
Install Rtools which is compatible with my R version
Add PATH: C:\Program Files\R\R-2.15.1\bin\x64;C:\Rtools\bin;C:\Rtools\gcc-4.6.3\bin
In cmd, enter: R CMD INSTALL packagename
Click "enter", done.
I had a lot of trouble getting this to work, and finally found the golden nugget on r-project (R doesn't like spaces in paths) so here's how I finally did all this:
I installed R to "c:\programs" instead of "c:\program files...". My final path to RSCRIPT.exe is "C:\Programs\R\R-2.15.2\bin\Rscript.exe"
I added that directory to my PATH, but that doesn't seem to help
RStudio is also installed under c:\Programs (e.g. c:\Programs\RStudio), but RTools is installed under the "c:\" root directory (e.g. c:\RTools).
I downloaded all the packages to "c:\downloads\r"
I opened a command prompt in "c:\downloads\r" and ran the R CMD install from this downloads directory, specifying the path to R
e.g. "C:\Programs\R\R-2.15.2\bin\x64\R CMD INSTALL colorspace_1.2-0.zip"
It appears that the CMD processor is Case Sensitive. You have to use INSTALL vs. install
Simple solution, use quotes:
c:> "C:\Program Files\WinZip\wzunzip.exe"
if you run this, you don't need to worry about the space in Program Files.
Hope this help.
I encountered a similar problem while trying to use SparkR from Windows Power Shell. Each time I would do ".\sparkR.cmd" (I was inside the folder containing this file), it would throw an error message like,
cmd is not recognized as an internal and external
command...blah...blah...blah.
I solved the problem by adding "C:\Windows\System32" to my PATH.
I restarted my system and then repeated the process and this time, I saw a new error,
R is not recognized as an internal and external
command...blah...blah...blah.
I tried all sorts of approaches, including the ones mentioned above. NOTHING WORKED, I was probably wasn't efficient enough to make it work.
Then I came across this place at code.google. I simply copied the R.bat onto a notepad, named it as R.bat. Kept it inside the folder where sparkR.cmd was located. For me it was,
C:\Apache\spark-1.5.1-bin-hadoop2.6\bin\
The I placed it on my PATH as :
C:\Apache\spark-1.5.1-bin-hadoop2.6\bin\R.bat
Restarted my laptop, opened my Power Shell as an administrator and typed :
.\R.bat help
It worked fine. Then I typed,
.\sparkR.cmd
and there it was.
It worked.
I hope it helps to people new to R. Thank you G. Grothendieck.
In the .bat file add a line of code specifying the path of the folder where R is installed and then give the path of the script as follows -
#ECHO OFF
PATH C:\Program Files\R\R-3.5.1\bin
R CMD BATCH D:\project_abc\helloworld.R
Following this, run the .bat file and you will see the code in the script will run smoothly.
In my case the issue was solved by using Edit instead of New while selecting PATH in the window below:
enter image description here
After selecting Edit I added the directory below:
C:\Program Files\R\R-4.0.2\bin\x64
This solved the issue in my case.
I'm trying to run R from iTerm on an OSX computer (OSX 10.11.6). When I enter R, it opens up an older version of R, from the path /Users/***/miniconda2/bin/R. I would like it to run, by default, an R version found at /usr/local/bin/R, without having to enter the full path every time. How would one go about changing the location of the default R?
Thanks for your help
This is likely due to the PATH variable preferring ~/miniconda2/bin before /usr/local/bin. I'm giving you a few options here to help understand why it is happening.
Let's assume your PATH looks like this:
/Users/me/bin:/Users/me/miniconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
Modify PATH
You could modify PATH to move /Users/me/miniconda2/bin after /usr/local/bin or remove it from PATH completely. The downside is that if you rely on other binaries in ~/miniconda2/bin they will no longer be found when executing them by name.
Move R out of the way
Another option would be to move ~/miniconda/bin/R out of the way, for example using
mv ~/miniconda/bin/R ~/miniconda/bin/R-miniconda
Afterwards R will be run from the next location in $PATH, but if you update miniconda2 it may return.
Link to R further up in the PATH (easiest/best)
Finally, you could make sure that there is an R executable in something that is further up the $PATH. This is probably the easiest and most effective option.
First, make sure you have a bin folder in your home directory. If this is not the case, create it using mkdir ~/bin and then restart the terminal. The restart should cause the code in ~/.profile to add that folder to your $PATH. You can verify by doing echo $PATH. If this is not the case, add the following line to your ~/.profile or ~/.bash_profile:
export PATH=$HOME/bin:$PATH
In the example at the top, the PATH already contains /Users/me/bin at the beginning of the line (highest priority).
Next, create a soft link to the R binary in the newly created folder:
ln -s /usr/local/bin/R ~/bin/R
You should now be able to execute R, which will prefer the softlink created, which will execute the one you like. If it does not work right away execute hash -r or restart the terminal.
Just in case you happen to be using RStudio Server (open source) or someone is looking for how to change the RStudio Server default version of R, here is what I found when trying to answer the same question:
Starting in RStudio Server 1.3 (the newest version is 1.4.1106, released February 22, 2021), a user’s preferred version of R can be specified in the rstudio-prefs.json file in the global-level /etc/rstudio folder or in the user-level ~/.config/rstudio folder.
See https://blog.rstudio.com/2020/02/18/rstudio-1-3-preview-configuration/ and https://docs.rstudio.com/ide/server-pro/session-user-settings.html for user setting options in newer versions of RStudio Server.
See https://support.rstudio.com/hc/en-us/articles/200716783-RStudio-Release-History for RStudio release history and https://www.rstudio.com/products/rstudio/download-server/redhat-centos/ for Red Hat downloads of the newest version of RStudio Server.
I use Emacs and/or Aquamacs on a Mac system to edit the R, latex, and html code. After upgrading OS X to el Capitan, R stopped working (searching for program: no such file or directory, R). I was wondering if anybody encountered the same problem and found the solution.
This is what I did and it solved the problem.
re-install R (the latest version at the time of writing this post is 3.2.4)
include (setq exec-path (cons "/usr/local/bin" exec-path)) in the .emacs.
/usr/local/bin is where the command line R is soft linked.
Of course if the R command is not found in /usr/local/bin but somewhere else, you should change the path in step 2.
I had to re-install R and all the packages after upgrading. To be able to do this step easily, save your installed packages in a file before upgrading to El Capitan. The packages have not actually been removed, they reside in
/Library/Frameworks/R.Framework/Versions/3.2/Resources/library (3.2 = version), so you can still find them, but some may be in your user library.
To save your list of packages:
my.packages = library()[[2]]
write.table(my.packages,file="my.packages.txt", row.names=F, col.names = T)
Then upgrade, re-install from R-3.2.2.pkg (or latest), then read the text file in my.packages and use install.packages(my.packages, repos='http://cran.us.r-project.org') and you should be good to go.
Regarding R under "El Capitan", you do not necessarily have to re-install it. You can find out what happened by listing the directory
ls -l /Library/SystemMigration/History/Migration-<UUID>/QuarantineRoot/usr/bin
(where <uuid> looks like 38CF2251-9593-48E9-BAA4-4880AA47E908). This is where the OS upgrade put the links that used to live in /usr/bin. Just create the same symlinks to R and Rscript as root:
cd /usr/local/bin
ln -s /Library/Frameworks/R.framework/Resources/bin/R R
ln -s /Library/Frameworks/R.framework/Resources/bin/Rscript Rscript
This assumes, of course, that /usr/local/bin is in your PATH.
New installations of R should be aware of the changes in El Capitan, cf. this R bug report.
Here is another solution: replace emacs with ``modified emacs''. It solves all the problems with Auctex (latex-preview-pane-mode) and R. It is also consistent with OS 10.11.
You can download it from: http://vgoulet.act.ulaval.ca/en/emacs/mac/
I had the same problem getting R to run on El Capitan. The problem is now solved. What follows is exacly what I tried. You might find some of the steps irrelevant but I've included them for the sake of completeness.
Tried reinstalling it via homebrew (mentioined above) and got an incompatible message concerning el capitan.
Loaded 'modified emacs' (mentioned above).
Visited the following link:
http://ftp.heanet.ie/mirrors/cran.r-project.org/bin/macosx/
then downloaded and installed:
(i) R-3.2.2.pkg
and ran the checksum command in Terminal as directed by the instructions.
(ii) XQuartz
4. Then in terminal, typed R
and it worked.
For the course I'm doing, other packages or libraries were needed. To load the package 'geonames, in Terminal type:
install.packages(c("geonames"))
A message will appear asking to select a CRAN mirror. Also another window will open with a list of mirrors, click one and OK.
Similarly, the package 'UsingR' was loaded by:
install.packages(c("UsingR"))
__end
I think the problem is that usr/bin is no longer writeable. And that's where programs like R and Rscript lived. On my system, it looks like usr/bin was moved to something like:
/Library/SystemMigration/History/Migration-XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX/QuarantineRoot/usr/bin
I suppose you can add that quarantined folder to your path as on my system everything seems to be working fine if executed from there.
I had the same problem. I'm not sure what's changed in El Capitan but adding the path to the R binary (/usr/local/bin on my system) to the exec-path in my .emacs file fixed the issue for me.
I am running RStudio on MacOS and need to use some custom command line tools like csvcut (part of csvkit) for a function that multiple people on our team will use on their machines.
If I run a system('pip install csvcut) (I am using this command as an example; normally, I’d run csvcut) from R in the terminal, it works (checks if the last version has been installed, etc.), just like if I do it from the command line terminal.
If I do the same thing from within RStudio:
> system('pip install csvkit')
sh: pip: command not found
If I do which pip in the terminal and copy-paste the address into RStudio, it works:
system('/anaconda3/anaconda/bin/pip install csvkit')
Requirement already satisfied (use --upgrade to upgrade): csvkit in /anaconda3/anaconda/lib/python3.4/site-packages
# etc.
^ that’s the output if I simply do system('pipinstall csvkit') from R in the terminal.
Unfortunately, I can’t even run which pip from within RStudio. (Also, I couldn’t automatically pip install csvkit for others’ machines, since it requires sudo access.) If there was a way to point RStudio to R’s path, that would be easier.
I found instructions on some website that said to create a .Renviron file and have a R_LIBS_USER=~/R/library line in it, but that didn’t help.
Try adding this line to your .Renviron file:
PATH=/anaconda3/anaconda/bin:$PATH