I have R script within a plain text file named "TestFile.R".
I am running RStudio. I want to use the Windows console (cmd.exe) to pipe "TestFile.R" directly into the "R Script" editor of RStudio, without launching a new thread of RStudio.
This command in the console does exactly what I want:
rstudio -f TestFile.R
The contents of "TestFile.R" go straight into the RScript editor of the existing thread of RStudio.
It assumes, however, that "TestFile.R" is in the "bin" folder of RStudio, and also that
cmd.exe is running within that folder.
But I want to be able to do this from anywhere on my computer, using a console command like:
pathToRstudio\rstudio -f pathToTestFile\TestFile.R
To give an example, on my computer, this command fails:
C:\"Statistical packages"\RStudio\bin\rstudio -f E:\"my project"\TestFile.R
By trial and error, I discovered these solutions:
1/ omit the "C:\" part
2/ avoid quotation marks in the pathToTestFile.
So this console command works fine:
"Statistical packages"\RStudio\bin\rstudio -f E:\myproject\TestFile.R
Of course, I still am very restricted ; my default folder has to be "C:\", and I cannot have spaces in the path to TestFile.R, even though spaces within the Rstudio path are apparently OK !?
Could somebody please explain to me how to write this command in a way that is completely generic with regard to path specification?
I want to be able to run it from any folder, and have TestFile.R in any other folder. I do not want hassles about folder names containing spaces.
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 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'm calling an .exe from R using system("script.exe object").
I get Warning: running command had status 127. I know it means the .exe file has not been found.
I'm on windows. When I use shell instead of system it works like a charm. However, I am designing a Shiny application that will be deployed in a Linux environment (shinyapps.io). This is why I need to use system.
EDIT
On Windows, it works with system(paste("cmd.exe /c", "script.exe object"), intern = FALSE, wait = TRUE) as suggested here. But not when I deploy the app (on Linux).
HINT
Locally on Windows, if I replace system with system2: system2(paste("cmd.exe /c", "script.exe object"), wait = TRUE), it raises the status 127 warning and the output is exactly the same as in my deployed app on Linux.
It's tough to create a reproducible example here but if needed I can try. Please tell me.
Context: basically the .exe is a black box (compiled C++ code) that takes a .txt file as input and outputs another .txt file. I am using R to dump the .txt file to the current working directory, then read back in the .txt file generated by the .exe (created in the current working directory, where the .exe file is stored).
Just add \" could solve you problem, e.g.
> setwd("W:/www/ADemo/")
> system(paste0(getwd(),"/Hi 2.exe"))
Hello, world.
> setwd("W:/www/A Demo/")
> system(paste0(getwd(),"/Hi 2.exe"))
Warning message:
running command 'W:/www/A Demo/Hi 2.exe' had status 127
> system(paste0("\"",getwd(),"/Hi 2.exe","\" "))
Hello, world.
Update:
The 127 error is usually seen when there is a space in the path. One also needs to worry about the input of the application, e.g. "/path A/A 2" --in-path "/home/A/B C/d 123.dta". Here are some update comments:
system(shQuote(paste0(getwd(),"/Hi 2.exe"))) is much more convenient.
At least in R 3.2.4, the manual of system() recommends to use system2() instead to avoid path problem under Win/Linux/OSX/.
Update 2:
For Linux user, I created a function to detect the given file in your working directory is executable or not:
chkpermission<-function(file, mode='0777'){
exe_list <- system("echo `ls -l | grep -E ^-.{2}x\\|^-.{5}x\\|^-.{8}x` | awk '{print $9}'", intern=T)
if(length(exe_list)==0){
stop("no file is executable");
##Make sure you know what you are doing here, add a+x permission:
## if (!(file%in%exe_list)) Sys.chmod(file, mode = mode)
}
return(file%in%exe_list);
}
I've tested it on GNU awk/grep. The 2/5/8 indicates the executable permission of [u/2]ser, [g/5]roup, [o/8]thers., one could change it to meet the requirement.
The problem actually stemmed from the fact that .exe files are executables for Windows only. It does not work out of the box on Linux environments (you can use WINE but in my case it is not possible because I am calling the executable from within R, I don't have any sudo rights or anything on the virtual machine used by the host of my app). So I compiled the c++ code I had using g++ on a Linux virtual machine and used the .out file rather than the .exe.
Then in my R script I just needed these two calls:
system("chmod a+x script.out") # to make Linux understand that the file is an executable
system("./script.out object") # to run the script
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 have an install.bat file and a resource folder. so long as these two files are in the same directory, if you run install.bat, it will install a my lwjgl game. so what im trying to do is make a self extracting file that when completed runs the launch.bat file. I have tried using iexpress, and got it working for the most part. i have added in all my files and such so it will extract to some directory and then i can run the install.bat file to get my program to work. thing is though, i want the exe i created with iexpress to launch install.bat when its finished. so, i tried using the option in iexpress that says it will execute a command when finished the "installation" (using quotes because its not the actual installation, just extracting the files to some directory specified by the user). when i get to the step where it says what i would like to execute during and after the "installation". during the installation i left blank. after the installation i chose the install.bat file. when i try to click next though, it tells me i must choose something for the command during the extraction. I don't have anything specific to do during the installation so i just said "echo." (without quotes). after i was done i tried running the installer. before it even prompted me for a folder to extract to, it told me that echo. could not be executed. so i went back into my installation (via a .sed file) and changed the "echo." to "pause". that didn't work either. i then read on another website that in order to run a file the way i would like to, i put the file name in both the during and after installation boxes. i tried doing that and it didn't work either. can anyone please help me?
If I understood your question correctly you will need to specify what the iexpress must do at the post install command option provided so that cmd.exe is used instead of command.com, eg:
cmd.exe /c filethatyouwanttorun.bat
Refer to the question: Create Batch file for iexpress.
You can use the SED file and then modify the self extraction directive. This will run the batch file that you wanted to run and then install the application. (If you have chosen the option to extract and run an installation in iexpress, a temp folder will be used for the extraction I suppose.)
I'm not sure I understand your question exactly but perhaps a few points would help:
If you want a "do nothing" command, you can use something like:
cmd /c echo.
There is no "command during the extraction". There's only an install program and a post install command. Both of these execute after extraction. If you only need to execute one batch file, put it in the install program line and leave the post install command blank.
You can't ask the user for an extraction path and execute a file. You can only do one or the other. (The install program could prompt the user and copy the files there, though.)