I am trying to call an Rscript I created in Rstudio in Git, but it says "Rscript not found"
$ Rscript processDineSafe
bash: Rscript: command not found
I have made sure I am in the right directory, and also that my directory has the file I am trying to call. I also tried to make sure R was added to the path but I wasn't sure exactly how to confirm that.
I am new to git and R so any help would be greatly appreciated!
Related
I have been trying to learn how to use my R scripts in a bash like Git, so I can run said script in a pipeline, but I am having trouble getting started. I am using a Windows 10 system, and using the Git Bash as my mock Unix bash.
Here is the link to the tutorial I am trying to learn off of:
http://swcarpentry.github.io/r-novice-inflammation/05-cmdline/index.html
As a super simple example of a script, I made a script called session-info.R in RStudio. The only code it contained was:
sessionInfo()
I then went to Git Bash, and making sure that I was in the same directory as the script that I just wrote, I typed this into the command line:
Rscript session-info.R
To which I got the error: "bash: Rscript: command not found"
Does anyone have any ideas to how I could fix this? I feel like this is a really beginner error, but I haven't been able to figure out for a little while. Thank you for your assistance.
I am trying to run a R script on Linux using Rscript command. However, it gives me an error stating that no such file or directory.
Weirdly, when I use command "less" on that R script, it works and displays the script on the screen.
Can anyone explaining this to me ?
I'm working with R for a while, and I always worked with Rstudio, I tried just now to run a Rscript command in terminal (I have a mac..) and I got this error-
>Rscript script.R
-bash: Rscript: command not found
when I tried to open R in the terminal I go the same error-
>R
-bash: R: command not found
I can run R code with the Rstudio and the R application, but I know there is a way to run R throw the terminal.
Did I miss something when I installed R on my computer? do I need to add R to my PATH?
thanks in advance!
Steps to run R script through Windows command prompt
Set the PATH variable for Rscript.exein the environment variables. Rscript.exe can be found inside bin folder of R. Set the path for Rscript.exe to use Rscript command in Windows command prompt. To check if Rscript.exe has been set environmentally or not, type Rscript in command prompt. The follwoing message should come.
Go to Command Prompt, set the path where your .R file is there.
Run the following command: Here abcd.R is present under Documents folder. So I set path and then run Rscript abcd.R
For those who stumbled upon this but use a mac, you might find this useful. I recently downloaded and installed R and RStudio through the CRAN site. I didn't do it through homebrew. Since I downloaded this install directly from the site, it DID NOT add the RScript executable to my /usr/local/bin directory.
I have locate on my mac so I did a quick lookup:
locate RScript
And I found it here:
/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/Rscript
What I had to do was create a symbolic link to my /usr/local/bin directory to get it to work:
cd /usr/local/bin
ln -s /Library/Frameworks/R.framework/Versions/4.0/Resources/bin/Rscript Rscript
Now I'm able to run Rscript through the command line. This may help someone else out there.
I am a bit lost when dealing with installing and using R. I installed R 3.0.1 from source and did the ./configure, make, make check, and make install as suggested. However I tried running R but it said that R wasn't in the /usr/bin folder. So I then copied the entire R-3.0.1/bin directory into my /usr/bin directory using cp. Now I'm getting a few errors regarding /usr/bin/env when trying to use RScript on a hello_world.R script I wrote from the O'Reilly R In a Nutshell book I store in a file hello_world.R the contents are below:
#! /usr/bin/env RScript
print("Hello World!");
Simple enough, but when I try to load it I get the following error:
$ ./hello_world.R
/usr/bin/env: RScript: No such file or directory
I'm not sure if this is a PATH problem or something, but when I search in my /usr/bin directory I do see the RScript file in there along with (R, BATCH, and the others associated with R programming language). Any help is greatly appreciated. Cheers.
You may be using an invalid command line option for Rscript in your shebang line.
For instance ...
#!/usr/bin/env RScript --vanilla
remove "--vanilla" (or other offending option) and rerun your script
#!/usr/bin/env RScript
I know you didn't put this in your example, but the solution may help others searching for the same issue.
Again, the good solution to this problem is very simple and clearly explained in the man page of env. The script should use the env command to invoke Rscript and not Rscript directly:
#!/usr/bin/env Rscript
some R code now...
But a script like this will read the user's .Rprofile among other things. When we want to have a vanilla R session (in order to start with a clean and controlled R), we must pass the option --vanilla. If you try something like
#!/usr/bin/env Rscript --vanilla
some R code now...
env will take the string Rscript --vanilla a the command to execute and will inevitably return the error message
/usr/bin/env: ‘Rscript --vanilla’: No such file or directory
In env's man page, there is an option called -S for splitting the strings. Its role is exactly to solve the problem above and use the first string Rscript as the command name, and the following strings (like --vanilla) as options to pass to Rscript.
The solution is therefore:
#!/usr/bin/env -S Rscript --vanilla
some R code now...
Put in the shebang line of your script #!/usr/bin/Rscript and it should work.
As a side remark if you want to keep up-to-date with the R versions from CRAN and not relying on the native R of your Linux distro (Ubuntu) then add the following line in your apt sources:
deb http://my_favorite_cran_mirror/bin/linux/ubuntu raring/
After that you can always use the apt system to install R which -I would agree with Jake above- it should be the preferable way to install R.
*Change the my_favorite_cran_mirror with a valid CRAN mirror that is close to you.
#! /usr/bin/env RScript
print("Hello World!");
Simple enough, but when I try to load it I get the following error:
$ ./hello_world.R
/usr/bin/env: RScript: No such file or directory
Here u make mistake is that instead of RScript write Rscript.
The syntax will be
#! /usr/bin/env Rscript
print("Hello World!");
Then run it it will work (y) all the best.
$./hello_world.R
I arrived at this question trying to understand this error message on a cluster computer where I did not have control over the R installation.
In general, when I converted Rscript in my makefile to /usr/bin/Rscript the error message no longer occurred.
I have been trying to execute a simple test.R
setwd("C:\Users\jdd\Documents")
test <- 2*6598
filename = "test.csv"
write.csv(test,file=filename)
Via the following command line command in Windows:
"C:\Program Files\R\R-2.15.2\bin\R.exe" CMD BATCH --vanilla --slave "C:\Users\jdd\Documents\test.R"
When I execute this I get the following error:
The system cannot find the path specified.
I have been trying to work out a solution on the basis of the provided error message, but failed so far. Wondering if somebody can help me so I can execute the script directly from the command line. Thanks
Thanks #sebastian-c! I tried to use RScript, which I investigated before. However, the problem was a different one. Appears that in my installation there is a R.exe and Rscript.exe file in .\bin, but also one in .\bin\x64. The first one is not working properly, but the second one is. The comment made by #Roland is very important as well, since once working I got this error message!
The following command did the job:
"C:\Program Files\R\R-2.15.2\bin\x64\Rscript.exe" "C:\Users\jdd\Documents\test.R"
and the corrected text.R is:
setwd("C:\\Users\\jdd\\Documents")
test <- 2*6598
filename = "test.csv"
write.csv(test,file=filename)
As mentioned here, it might has something to do with 64bit version of R.
The problem is that Rscript.exe itself is attempting to access a missing file on the system. The obvious fix is explicitly add 'x64' to the path of the other Rscript.exe that was installed:
"C:\Program Files\R\R-2.15.2\bin\x64\Rscript.exe" --version
R scripting front-end version 3.0.2 (2013-09-25)