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.
Related
shell_exec("Rscript C:\R\R-3.2.2\bin\code.R ");
This is the call to script.On calling the above script, the error occurs.
I am trying to call my R script from the above path but no output is being shown. While checking the error logs of PHP, it says 'Rscript' is not recognized as an internal or external command, operable program or batch file.' The script is working fine on the Rstudio but not running on the command line.
Add the Rscript path to your environment variables in Windows:
Go to Control Panel\System and Security\System and click Advanced System Settings, then environment variables, click on path in the lower box, edit, add "C:\R\R-3.2.2\bin"
Restart everything. Should be good to go. Then you should be able to do
exec('Rscript PATH/TO/my_code.R')
instead of typing the full path to Rscript. Won't need the path to your my_code.R script if your php file is in the same directory.
You need to set the proper path where your RScript.exe program is located.
exec ("\"C:\\R\\R-3.2.2\\bin\\Rscript.exe\"
C:\\My_work\\R_scripts\\my_code.R my_args";
#my_args only needed if you script take `args`as input to run
other way is you declare header in your r script (my_code.r)
#!/usr/bin/Rscript
and call it from command line
./my_code.r
If you are running it in Git Bash terminal, you could follow a revised version of the idea suggested by #user5249203: in the first line of your file my_code.R, type the following
#!/c/R/R-3.2.2/bin/Rscript.exe
I assumed that your path to Rscript.exe is the one listed above C:\R\R-3.2.2\bin. For anyone having a different path to Rscript.exe in Windows, just modify the path-to-Rscript accordingly. After this modification of your R code, you could run it in the Git Bash terminal using path-to-the-code/mycode.R. I have tested it on my pc.
I faced the same problem while using r the first time in VS Code, just after installing the language package (CRAN).
I restart the application and everything worked perfectly. I think restarting would work for you as well.
I'm trying for my first time to run an R script from command line on WINDOWS to automate calculation with another program. So I made my R script using R studio and saved it a .bat file with this line
C:\Program Files\R\R-4.0.2\bin CMD BATCH C:\my_directory\my_script.R
Then I putted the script and files the script have to be executed on in the same directory, the one that contains files to run also the program I need. I came throught command line in that directory and I executed the batch file but it doesn't work. I have this as a error message:
"C:\Program Files\R\R-4.0.2\bin"it is not recognized as an internal or external command,
an executable program or batch file.
Where I am wrong? thank you!
You should use Rscript instead, assuming its in your PATH.
E.g.
Rscript C:\my_directory\my_script.R
Or a single expression
Rscript -e "print(123)"
I am trying to run a Windows executable file from R. I have managed to open the executable file from R using the command:
system2('cmd', args=c('/c', '"C:/Program Files (x86)/UIFormModel.exe"'))
To run the executable file, I need to import an Excel file by clicking on the button “Load Settings File” (see figure below). Thus, the button is part of the executable file.
How can I do this from R ?
I have tried this command but it does not work:
system2('cmd', args=c('/c', '"C:/Program Files (x86)/UIFormModel.exe"', '"F:/template_LHS1.xlsx"'))
'C:/Program' is not recognized as an internal or external command,
operable program or batch file.
Warning message:
running command '"cmd" /c "C:/Program Files (x86)/UIFormModel.exe" "F:/template_LHS1.xlsx"' had status 1
Several points:
normally one does not have .exe files directly under C:\Program Files (X86) so first double check the path name. I suspect it is not as in the question but is something like the one shown below.
note the quoting used below
are you sure that the program accepts a command line argument as an alternative to its GUI? Can you run it from Windows cmd line? If not you could write an autohotkey (see AutoHotKey section below) or autoit script to control it and launch that from R.
if it does accept an argument ensure that the program allows forward slashes -- if not use backslashes
cmd line argument accepted
If the program accepts a command line argument then try this code:
system2("C:/Program Files (x86)/UIFormModel/UIFormModel.exe", "F:/template_LHS1.xlsx")
Another way is:
shell('"C:/Program Files (x86)/UIFormModel/UIFormModel.exe" F:/template_LHS1.xlsx')
For example, using the free CSVfix I was able to run the following and found that they worked:
system2("C:/Program Files (x86)/CSVfix/CSVfix.exe", "help")
shell('"C:/Program Files (x86)/CSVfix/CSVfix.exe" help')
See ?system2 and ?shell for other arguments you may wish to use.
AutoHotKey
If the program does not accept command line arguments then this sample AutoHotKey script launches WinMerge, a free file comparison GUI for Windows, comparing the WinMerge executable to itself. This has the effect of generating a popup warning and the AutoHotKey script dismisses that warning message by sending an Enter keystroke to the WinMerge window.
Be sure AutoHotKey and WinMerge are installed, that the script below is in a text file, test.ahk, in the current directory, the one given by getwd(), and then from the R console run:
shell("test.ahk")
Here is the test.ahk script:
exe = "C:\Program Files (x86)\winmerge\winmergeu.exe"
Run %exe% %exe% %exe%
WinWait WinMerge
; dismiss the dialog warning that both files are the same
Send {Enter}
If you go this route this script will need to be modified or rewritten in ways that will be specific to your program.
I've been trying several alternatives, but I've not successfully called an executable with a parameter. Nevertheless I can suggest a workaround using a .bat file:
system2("cmd.exe", input='"D:/workspace/execute.bat"')
Where execute.bat may contain something like:
C:/Program Files (x86)/UIFormModel.exe F:/template_LHS1.xlsx
My goal is to use PowerShell to schedule the sourcing of an R script.
My current work flow is that I open RStudio, click the "Source" button in the upper right corner. Then I wait until it's finished, and close RStudio. I change nothing in the R script.
In PowerShell I've been using its Register-ScheduledJob cmdlet to kick off C# programs on a daily schedule. And here's the problem, I can't find an example of effectively using PowerShell to source an R script.
I believe the PowerShell script should probably use the Invoke-Expression cmdlet. But I'm not 100% sure.
To no avail I've tried this:
Start-Process "C:\Program Files\R\R-3.2.4revised\bin\x64\Rterm.exe" -RedirectStandardInput "C:\MyScript.R"
Also, I'd like to avoid the solution that uses CMD BATCH as that's defeating the purpose of using PowerShell.
If just sourcing the R script is what you're looking for then one way to do is something like this
& "C:\Program Files\R\R-3.1.1\bin\Rscript.exe" "C:/Program Files/R/R-3.1.1/tests/demos.R"
where "C:\Program Files\R\R-3.1.1\bin\Rscript.exe" is path Rscript in your local R installation and "C:/Program Files/R/R-3.1.1/tests/demos.R" is path to script you'd normally source() directly in RStudio.
One thing to keep in mind is depending on location of files your R script needs you might need to adjust your script with appropriate setwd()
I'm trying to run a R script through a .bat file. When I run myself the commands line by line it works. But when I try to run the .bat file, it doesn't works.
This is the .bat file
cd "C:\Program Files\R\R-3.1.2\bin"
R CMD BATCH "C:\Users\Administrator\Downloads\testa_vps.R"
This is the R script
setwd('C:\Users\Administrator\Documents')
file.create('mycsv.csv')
I'm not an expert with Windows and generally try to stick to Unix-like systems for things like this, but I have found that using programs non-interactively (e.g. via .bat files) is usually less error-prone when you add the appropriate directories to your (user) PATH variable, rather than cding into the directory and calling the executable from within the .bat file. For example, among other things, my user PATH variable contains C:\PROGRA~1\R\R-3.0\bin\; - the directory that contains both R.exe and Rscript.exe - (where PROGRA~1 is an alias for Program Files which you can use in an unquoted file path, since there are no spaces in the name).
After you do this, you can check that your PATH modification was successful by typing Rscript in a new Command Prompt - it should print out usage information for Rscript rather than the typical xxx is not recognized as an internal or external command... error message.
In the directory C:\Users\russe_000\Desktop\Tempfiles, I created test_r_script.r, which contains
library(methods)
setwd("C:\Users\russe_000\Desktop\Tempfiles")
file.create("mycsv.csv")
and test_r.bat, which contains
Rscript --vanilla --no-save "C:\Users\russe_000\Desktop\Tempfiles\test_r_script.r"
Clicking on the Windows Batch File test_r ran the process successfully and produced mycsv.csv in the correct folder.
Before running test_r.bat:
After running test_r.bat:
I've never worked with a Windows server, but I don't see why the process would be fundamentally different than on a personal computer; you just may need your sysadmin to modify the PATH variable if you don't have sufficient privileges to alter environment variables.
As already suggested by #nrussel in the comments you should use RScript.exe for this.
Create a file launcher.bat with the following content:
cd C:\Users\Administrator\Documents
Rscript testa_vps.R
In addition, add C:\Program Files\R\R-[your R version]\bin\x64; or C:\Program Files\R\R-[your R version]\bin\i386to the System PATH variable in the Environment Variables menu depending if you run R on a 64-bit or 32-bit system.
I just tested the approach above successfully on a Windows Server 2008 64-bit system and mycsv.csv got created as expected.
EDIT
One important point I forgot to mention is the following: You need to specify the path in your R file in the setwd() call using \\ instead of \.
setwd('C:\\Users\\Administrator\\Documents')
Here is a screenshot of the successful run on the Windows 2008 server:
Note: I added cmd /k to the .bat file so that the cmd window stays open after clicking on the file.