I tried to run an Rscript file from my ubuntu terminal on the server using the code:
Rscript etl/ConceptTables/loadTables.R mimiciii"
The file is located in stated directory below but I need to run the script from the root directory. However, it is saying this file does not exist but it clearly does. I also tried running this by entering the R environment first but instead, I get:
"Error: Unexpected symbol in "etl/ConceptTables/loadTables.R mimiciii"
I am following instructions from this mimic-omoop ETL on github here: https://github.com/chichukw/mimic-omop/blob/master/README-run-etl.md and I already created the cpg file with my username and database name. Could anyone clarify what I am doing wrong?
Try using the full path of the file. The error you have posted is "Unexpected symbol"
Could be because you have added a double quote at the end of mimiciii. Or is it a mistake while posting the question?
If you are using double quotes for the path, ensure that it is " and not “.
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 have a R script that should change the working directory using setwd().
My code:
setwd(file.path(work_dir, database_dir, study))
I can pause my script just before this line is supposed to execute (using browser()) enter the code into the console without issue, but whenever the line is executed from the script I get the error box stating that there is an "error while opening file: The system cannot find the file specified." Within my script before calling the setwd, I confirmed that the path exists using file.exists(file.path(work_dir, database_dir,study)). I also restarted R studio and closed and reopened all of my scripts to make sure that was not causing the problem.
Does anyone have any other suggestions for me to try?
Posting how I resolved the issue:
The script that changed the directory (I will call this script 2) was called by another script first (I will call this script 1). script 1 and script 2 are in the same directory, but different directories from where I where I was trying to change. script 1 called script 2 using source("script2.R"). When I changed this to source(file.path(work_dir, "script2.R")) I no longer had issues with the setwd() command. My GUESS is that when I changed directories Rstudio "forgot" what script it was supposed to be executing and that is why I got a "no file exists" error.
If anyone has any other thoughts - please share!
I'm trying to create a batch file to run an R script for me automatically on Windows 7.
Batch file:
"C:\Program Files\R\R-3.2.3\bin\Rscript.exe" CMD BATCH "C:\Users\<my username>\Documents\R\Script Testing\script.R"
pause
R script:
write.csv("hello", "automatic_output.txt")
This script works when I run it in R, but when I try to run the .bat, I get this error:
Fatal error: cannot open file 'CMD': No such file or directory
This happens regardless of whether I paste the code into the command prompt, run the .bat as administrator, or schedule the task.
I tried following the advice given in this thread:
Exporting .csv from R & Batch file
but am seeing the same behavior.
I also used the Windows search to try to find "automatic_output.txt" in case it was being stored in an unexpected location but no results came up.
Lastly,
https://stackoverflow.com/a/23514987 seemed to suggest that I could omit the "CMD BATCH", and when I do I no longer get an error, but automatic_output.txt is still not produced.
Any ideas?
As Thomas pointed out, I needed to change "Rscript.exe" to "R.exe". For future googlers, here is the line of code that worked:
"C:\Program Files\R\R-3.2.3\bin\R.exe" CMD BATCH "C:\Users\<my username>\Documents\R\Script Testing\script.R"
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.
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.)