I am new to R script.
I found at the beginning of the R script,
#!/conda_env/myenv/bin/Rscript
library('httr')
May I know what does it mean #!/conda_env/myenv/bin/Rscript?
What happen if I do not add #!/conda_env/myenv/bin/Rscript?
Thank you
The symbol #! is known as a shebang.
When a script starts with #!/conda_env/myenv/bin/Rscript you can run it from your terminal without specifying that it needs Rscript. If your file is called myfile.R you can run it with
/path/to/myfile.R
If you remove this line you have to run the file with the command
/conda_env/myenv/bin/Rscript /path/to/myfile.R
Edit: If /path/to/myfile.R cannot run you must make it executable. In your terminal this can be done with the command chmod u+x myfile.R.
Related
I'm trying to run an R script through the command prompt. My operating system is Windows 10. I'm having trouble running the code because there is a space in the file path of my argument. This is what I paste into the command prompt.
"C:\Program Files\R\R-3.4.3\bin\Rscript.exe" "C:\Users\Scott\Google Drive\RScriptsB\Bundle_Runner.R"
I get this error:
The filename, directory name, or volume label syntax is incorrect.
However, when I run it using a file path with no spaces, it runs fine.
"C:\Program Files\R\R-3.4.3\bin\Rscript.exe" "C:\Users\Scott\Desktop\Bundle_Runner.R"
The same behavior happens when I schedule the task through Task Scheduler: it doesn't work with the space, and it works when I remove the space from the file path.
I'm using Google Drive to sync work from multiple computers, so I'd like to be able to run my scripts using the file path with a space.
Any solutions?
FOR %%a IN ("C:\Users\Scott\Google Drive\RScriptsB\Bundle_Runner.R") DO "C:\Program Files\R\R-3.4.3\bin\Rscript.exe" %%~sa
would be my approach - the problem appears to be with R, not cmd.
Try this:
C:/PROGRA~1/R/R-3.4.3/bin/Rscript.exe "C:\Users\Scott\Desktop\Bundle_Runner.R"
Or
C:/PROGRA~1/R/R-3.4.3/bin/Rscript.exe C:/Users/Scott/Google~1/RScriptsB/Bundle_Runner.R
This is possibly related to an error reported at r-devel ("[Rd] Bug in RScript.exe for 3.5.0", https://stat.ethz.ch/pipermail/r-devel/2018-April/075869.html) that has been fixed the next day.
Perhaps the problem was already present in R 3.4.3 (you are using in your question).
Proposed workaround:
...add an extra first argument that has no space in it, e.g. Rscript --vanilla "foo bar.R"
To minimize the impact caused by --vanilla you could use
Rscript --no-save "foo bar.R"
instead (which just does not save the workspace at the end of the session).
I am running a script that starts as follows:
#!/usr/bin/env Rscript
#./geneiase -t static -i mydata.tab
If I run the script on my data directly in the command line, it starts without errors or warnings.
But the program is very demanding computationally so I need to submit my jobs to a cluster using a job scheduler called Slurm.
When I write the exact same expression (as in the second paragraph) within the batch job file, and then I submit the job using sbatch, it is immediatelly terminated and does not return any error or output that can help me understand the problem.
I think it has to do with having Rscript in $PATH, but even though I added the directory where Rscript is located to $PATH by: PATH=$PATH:path/to/R/build/R-3.4.0/lib64/R/bin, the problem remains.
Is there a way that I can make Rscript be run in a Slurm batch job?
You'll need to keep the environment of your SLURM script as bash
#!/bin/bash
Since you can run your R script from the command line, it likely means the path to R is already included in your $PATH. On the command line, you might already do something like:
Rscript ./path-to-script/script
To run R from within your SLURM script, it's the same as running from the command line:
Rscript ./path-to-script/script
I am on a windows machine and want to run a file called main.r so in the command line I put:
"C:\Program Files\R\R-3.0.2\bin\r.exe" CMD BATCH "C:\Users\myname\Desktop\R Projects\soultion\MAIN.R"
when I run this nothing happens. The command line just goes to the next line.
Can you advise what I am doing wrong?
Thank you.
That is what is supposed to happen. Output gets piped to MAIN.Rout in your case. If you want the output to display in the terminal use Rscript instead of R CMD BATCH.
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 want to run a R script file (.r) using batch file.
If R.exe is in your PATH, then your windows batch file (.bat) would simply consist of one line:
R CMD BATCH your_r_script.R
otherwise, you need to give the path of R.exe, so for example:
"C:\Program Files\R\R-2.13.0\bin\R.exe" CMD BATCH your_r_script.R
you can add certain input arguments to the BATCH command, such as --no-save, --no-restore
so it would be
R CMD BATCH [options] your_r_script.R
more info on options, etc at http://stat.ethz.ch/R-manual/R-devel/library/utils/html/BATCH.html
Note: R uses the command "BATCH" to non-interactively evaluate a script located in a file. Here we are running the command "BATCH" from a windows .BAT file, but that's merely a coincidence.
An answer to another question suggests using Rscript.exe, so your batch file would contain:
"C:\Program Files\R\R-3.0.2\bin\i386\Rscript.exe" your_script.R
pause
It is a good idea to add R to the windows environment path. In a comment in this question #chase gave a link that explains how to set the path on windows 7. Once R is added to the windows path, your batch file should become simply :
Rscript.exe your_script.R
pause
You can also directly call a R command by using the -e flag. For example this batchfile will tell R to set its current working directory to Documents, then it will print the working directory:
Rscript.exe -e setwd('Documents');getwd()
pause
I struggled with the syntax with the answers below, but this worked for me in the .bat file:
C:\Windows\System32\cmd.exe /k ""path to Rscript.exe"
"path to .R script""
Be sure to place both the path to Rscript.exe and the script in "" together and separately as above.
I doubt you will be able to run it using a batch file.
http://www.fileinfo.com/extension/r
Most known programs that use .r files do so for source code files it looks like. You will probably have to compile it using the program it was written for. I guess you could use a command line compiler from a batch file, but I don't know what language or applications you are using.
If you post the script file or give more information about it, we could probably help you better.