I have an R script that gets data from databases on another server and brings it into my database. I have it saved as "dataimport.R"
I followed a few answers from here and from other websites and created a batch file like this:
"C:\Program Files\R\R-3.4.0\bin\R.exe" CMD BATCH --vanilla --slave "C:\dataimport.R"
This is not working. The cmd window opens up but the tables are not recreated and I dont get any error. I wanted to run the Task Scheduler to automate the process. Any ideas on how to fix this?
I kept at it and interestingly the answer to this was this:
"C:\Program Files\R\R-3.4.0\bin\R.exe" "C:\dataimport.R"
I dont know the reason for this but as long as it works.
I've had loads of problems with this, but finally managed to get it to work. To be more comprehensive, here are some of the things I've tried (in case one of these work for other persons):
#echo off, R CMD BATCH C:\myfolder\script.R
R CMD BATCH C:\myfolder\script.R
Using the package taskschedulerR (somehow didn't work overnight)
Used the answer provided above ("C:\Program Files\R\R-3.4.0\bin\R.exe" "C:\dataimport.R")
and all kinds of variations and combinations off these. (can't remember them all exactly)
What finally worked was:
Make an R script and save it (C:\myfolder\Test.R for example)
Through notepad, fill in: "C:\Program Files\R\R-3.5.2\bin\x64\R.exe" CMD BATCH "C:\myfolder\Test.R" (also tried Rscript.exe, didn't work for me).
in Windows Task Scheduler (v1.0) do 'Create task'
fill in time triggers.
in Actions, make an action with Start a program and in the Program/Script line provide the location where your bat script is. C:\myfolder\Test.bat
in the Start in (optional) line: enter C:\myfolder\
Note: both your .bat file and .R script are in the "C:\myfolder" folder.
Related
I wanted to use a Windows .bat file to run several R scripts and schedule it using windows scheduler.
However, when I test using windows scheduler, everything executes but the files that the R scripts should create are never created. Instead, when I double-click on the .bat file itself it works fine. My goal is for several scripts to just run overnight without me going in and running each one of them manually one-by-one.
If I were to add a second line to the .bat file that would make it run a second script, would this execute only after the first is complete? If not, would I be able to delay the second until the first finishes somehow?? For instance, my .bat file looks like this:
"C:\Program Files\R\R-3.4.2\bin\x64\R.exe" CMD BATCH C:\Users\gma\Desktop\R_Task\script1.R
"C:\Program Files\R\R-3.4.2\bin\x64\R.exe" CMD BATCH C:\Users\gma\Desktop\R_Task\script2.R
I used the answer provided by #Gautam (R taskscheduleR not executing script) to get this far
I'm trying to basically run the following .bat file as a scheduled task, while also logging errors in a .txt file:
In the 'program/script' box, I just have cmd. Then in the add arguments box I have:
/k ""T:\Some_folder\mybatchfile.bat" >>"T:\somelog.txt" 2>&1"
This had been working just fine originally before I tried to add the log function and calling cmd explicitly as seen in several posts, but I'd really like to add this function. I'm using /k for now so that I can watch the cmd window as things happen, but plan to replace it with /c so it closes when its done.
I tried many permutations of where my quotation marks are but am not having a lot of luck. I'm also intentionally using >> vs > in order to append the log, not overwrite it.
The contents of the .bat file are basically:
"C:\RDirectory\R.exe" CMD BATCH "T:\Some_folder1\Preworkforbatch.R"
copy T:\Some_folder2\some_data.csv "C:\Users\ABC1\Another_folder"
copy T:\Some_folder3\some_more_data*.csv "C:\Users\ABC1\Another_folder"
I'm wondering if part of it is that T is a network folder that is mapped? Thanks for your help.
edit:
Here is more info on the task:
"T:\Some_folder\mybatchfile.bat" >> "T:\somelog.txt" 2>&1
When redirecting the output of a batch file to a log file you will not see as much output in the cmd window. You have to repeatedly open, close, open the log file to see your progress. Use the title command in your batch to display progress info in the cmd window.
title This is %~F0. The time is %time%. The date is %date%. SLEEP 3600 FOR :RECORDRADIO
Ok this ended up working for me, by editing the batch file itself, and just running the batch file (not cmd explicitly) in the task scheduler:
mybatchfile.bat:
#echo on
"C:\RDirectory\R.exe" CMD BATCH "T:\Some_folder1\Preworkforbatch.R" >> "C:\Users\ABC1\Logfolder\mylog.txt" 2>&1
copy T:\Some_folder2\some_data.csv "C:\Users\ABC1\Another_folder" >> "C:\Users\ABC1\Logfolder\mylog.txt" 2>&1
copy T:\Some_folder3\some_more_data*.csv "C:\Users\ABC1\Another_folder" >> "C:\Users\ABC1\Logfolder\mylog.txt" 2>&1
Writing the log file to the network was causing errors. Writing to the local computer solved this issue. Not using double quotes also was key, instead just quotes around the file/path. This setup gives me an output for each line, so for every line 2>71 shows up, I get an output if there's an error or a completion message.
This is what the task scheduler looks like:
I'm trying to get batch mode working for R on Windows 10. The ultimate goal is to run many iterations of some R code in batch on an external server.
I successfully installed bash (unix wrapper for windows 10?) on my cmd prompt. I am working through a tutorial on using batch. I'm not sure if I want this to run through cmd or through the r code directly? https://github.com/gastonstat/tutorial-R-noninteractive/blob/master/02-batch-mode.Rmd
Via the tutorial I am working on testing batch/bash with simple code myscript1.R. Then the code I enter into cmd promp/bash looks like:
R CMD BATCH "F:/Google Drive/Documents/batch/myscript1.R" "F:/Google Drive/Documents/batch/myscript1-output.R"
Currently the closest I get in the cmd/bash is that an output file is created in the right folder but blank and I am told \usr\lib\R\bin\BATCH: cannot create myscript1-output.R: Permission denied.
I have done everything possible to allow full permissions to all users and not sure what is going on. Can anyone who knows how to use batch mode or bash in R for windows advised me?
Thank you
Answer here thanks to Phil. I did not need to use "Bash" through Ubunto... I think.
Instead, I just needed to call the CMD BATCH through regular cmd with three parts:
the directory of my R.exe: "C:\Program Files\R\R-3.5.3\bin\x64\R.exe" (replace version)
CMD BATCH
directory of the project file/script: "F:\project_folders_batch\myscript1.R"
directory of the desired output (so it doesn't default to C/users/username). In this case, I output to the same folder as the script: "F:\project_folders_batch\myscript1-output.R"
Also, in case you are outputting plots or anything (I was), go ahead and cd (change directory) to the project folder before you do this. Final result in 2 steps:
cd /d "F:\projectfolder\batch"
"C:\Program Files\R\R-3.5.3\bin\x64\R.exe" CMD BATCH "F:\projectfolder\batch\myscript1.R" "F:\projectfolder\batch\myscript1-output.R"
Also mind your antivirus... it blocked access a few times.
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've just set up an R script to run on my Windows machine - I'm trying to have it save a dataframe on the working directory (which I know from getwd()).
I can see from the Task Scheduler that the script must be running as saves the last run time, however when I check the wd for new time stamps on the dataframes I'm trying to save, they haven't updated? (I save over them each time, or at least that's what I'd like to do, I manually saved them in there to start with).
I'm using this on the scheduler:
C:\Program Files\R\R-2.13.1\bin\R.exe" CMD BATCH --vanilla --slave “C:\my projects\my_script.R
That appears to be working, but can anyone offer a reason as to why the script that I call doesn't seem to be saving my NEW DF to the wd? I'm using this command to save the DF:
write.table(m23,file="m23.csv",sep=",",row.names=F)
so DF m23 should get updated everyday in the wd when the scheduler calls the script at 6am?
Paul.
Are you sure you know what the current working directory is when the scheduler runs the script? My guess is it might not be what you think is it. I would look at the answers to this question: Rscript: Determine path of the executing script, especially the suggestion about using commandArgs to figure out where you are. Or you can explicitly set the working directory in your script with setwd()