I have the following added to my system path on Windows 10: C:\Program Files\R\R-3.4.3\bin\x64
Then I tried running from cmd prompt ~:> R myscript.R
ARGUMENT 'example_batch.R' ignored
It proceeded to an interactive session without any execution.
No idea how it seemed to work in this answer. I would prefer something this simple, as it is in Python.
The following works R -e "source('myscript.R')"
But I'll never remember this when I need it.
Lucas's solution gave me an error when run in Powershell/Windows termianl (which is now the default on Windows 11). It seems that when the executable dir is inside quotation marks (""), Powershell treats it as a string.
To execute Rscript.exe in Powershell, you need to add & before the dir
& "C:\Program Files\R\R-4.2.2\bin\Rscript.exe" "C:\PATH\TO\SCRIPT.r"
The best way I've found is by executing Rscript.exe (it's installed with R.exe inside R directory).
You can do:
"C:\Program Files\R\R-3.6.0\bin\Rscript.exe" D:\path\to\yourRfile.r arg1 arg2 arg3
The quotation marks ("") are necessary because dir name Program Files has space between it and Windows CMD wouldn't recognize it without quotation marks.
If you don't want to write R path, you can put R Path to your windows PATH environment variable. This way you could run like:
Rscript.exe D:\path\to\yourRfile.r arg1 arg2 arg3
If you have doubts how to add R path to Windows PATH environment variable, you can follow these instructions (they are for adding Java to PATH, but you can use for R, the idea is the same).
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 often find it more useful to run R on the command line (windows). However when I try it in Powershell I tend to run into problems, but this is easily overcome by first running cmd and then it works.
This is the error I get when I do R CMD BATCH
Invoke-History: A positional parameter cannot be found that accepts the argument 'BATCH'
I later realised that r is an alias that returns the immediate past command, hence my inability to run R.
Subsequently, I found that using the full filename for the executable (i.e. R.exe) or using Rcmd.exe (i.e. Rcmd BATCH ...) worked.
However, I'm just curious, is there a work around, in case one runs into similar conflicts?
To start R in powershell:
R.exe
The workaround would be fully defining your calls.
& "path\to the\r.exe" arg1 arg2 etc
Alternatively,
$P = #{
FilePath="path\to the\r.exe"
ArgumentList=#('arg1','arg2')
}
Start-Process #P
I ran into this problem on linux, where there is no file extension for executables, so that didn't help, but still there are two options:
/usr/bin/R if it is installed in the usual location
Start-Process R (the start-process cmdlet does not need to be capitalized)
In windows 7 at run prompt, this command succeeds in launching the .exe with the the optional input file "test2.dat"
c:/Program Files (x86)/IEUBKwin1_1 Build11/IEUBKwin32.exe k:/Project/EPA.Pb.IEUBK/batch.io/input/test2.dat
I want to do the same thing from within R.
In R, this command succeeds in launching the same .exe
shell.exec("c:/Program Files (x86)/IEUBKwin1_1 Build11/IEUBKwin32.exe")
But I've been unable to find a solution within R that will launch the .exe with the optional input file. I've looked at shell(), shell.exec() and system() but I could not find the right incantation that will pass the optional input file to the .exe.
Any thoughts?
Typing into the normal cmd.exe-promt a command including spaces as in C:\Program Files (x86)\... does not work:
The Command "C:\Program" could not be found.
Typing in the same command with double quotes does work. E.g.:
"C:\Program Files (x86)\7-Zip\7z" -a ...
To get it to work in R, you can use single quotes (') to mark a R string and double quotes (") for the command itself. Actually, you have the possibility of three different quotes to use (backtick is the third one `, see here for more information). Or you use escapes as mentioned in the answer of #Frank.
system('"C:/Program Files (x86)/IEUBKwin1_1 Build11/IEUBKwin32.exe" k:/Project/EPA.Pb.IEUBK/batch.io/input/test2.dat')
In addition ?system mentions not just to use shell in windows but also system2 as alternative:
...This means that it cannot be assumed that redirection or piping will work in system (redirection sometimes does, but we have seen cases where it stopped working after a Windows security patch), and system2 (or shell) must be used on Windows.
But for me system works totally fine not using piping or redirection.
shell.exec() is used for opening files associated in your OS.
in your case, the shell command should be preferred but you need to take care of spaces in your filenames and mask quotaion marks.
Please try:
shell("\"c:/Program Files (x86)/IEUBKwin1_1 Build11/IEUBKwin32.exe\" k:/Project/EPA.Pb.IEUBK/batch.io/input/test2.dat")
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.
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.