This post will allow you to impress your boss with your strong work ethic by enabling Windows R users to schedule late night tasks. Picture it, your boss gets an email at 1:30 in the morning with the latest company data as a beautiful report. I’m quite sure Linux and Mac users are able to do this rather easily via cron. Windows users can do this via the Task Scheduler. Users can also interface the task scheduler via the command line as well.
As this is more process oriented, I have created a minimal example on GitHub and the following video rather than providing scripts in-text. All the scripts can be accessed via: https://github.com/trinker/Make_Task User’s will need to fill in relevant information (e.g., paths, usernames, etc.) and download necessary libraries to run the scripts. The main point of this demonstration is to provide the reader (who is a Windows user) with a procedure for automating R tasks.
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Thank you for this. Two points: To find the task scheduler, you can just search for “task sch” in the search part of the start (or whatever that windows button thing is called!) I forget if this existed for xp though…
Second point is a pro-tip, on various machines I have had inconsistent behavior with whether “R.exe” or “Rscript.exe” is in the “path” environment variable, (so simply using “R CMD BATCH” will not find the R.exe to run.) Ditto for basically every program I’ve ever installed on windows. If that is the case, you can just call the exe file directly with the full path name to both the exe file and the “.R” file (enclose in double quotes if spaces in either path).
(You can add R.exe to the path environment, but that is just as annoying and limits portability to new machines.) This advice basically extends to any automated task you want to do in windows, figure out the command line prompts, put them in a plain text “.bat” file, and then make a scheduled task. If whatever program you call is in the path environment, and the bat file is in the same folder as the “.R” file, you don’t need to specify the paths at all.
@apwheele Thanks for the additional info.
For the record apwheele is referring to using: “C:\R\R-3.2.2fibinfix64\R.exe” CMD BATCH C:\Users\Tyler\Desktop\Make_Taskfitask.R as seen http://www.statmethods.net/interface/batch.html
Very cool – thanks 🙂
Hello,
I have a problem when I run this line in R (scheduled or manually):
rmarkdown::render(“apple_microsoft.Rmd”, “all”, output_dir = “reports”)
As the result I get message
Error: pandoc version 1.12.3 or higher is required and was not found.
But when I run in RStudio manually everything is works.
Anyone has ideas how to solve this?
Thank you.
This really is an rmarkdown issue. There could be any number of issues you have but I suspect from the info you gave the followig is the issue: http://r.789695.n4.nabble.com/Apply-rmarkdown-render-outside-the-RStudio-don-t-find-pandoc-td4696190.html For more specifics on a problem with render I’d ask the folks at RStudio https://github.com/rstudio/rmarkdown/issues
Thnk you so much for your help
First, Thanks for sharing this post. I have been trying to implement something like this in a while but was having trouble with the email section. Second, I have two questions;
1- Can I email to multiple users at once?
2 – The packages that I downloaded while running task.r now reside on my machine locally or they have dependencies on your website or github still?. A more straight forward question, If you delete all the code from github today, I would still be able to send automated email and reports? Thanks and sorry for the naïve questions.
Yes and Yes (unless you delete gmailR locally) but there are (as I say in the video) better ways to email. See https://kbroman.wordpress.com/2014/09/03/notifications-from-r/
Thanks! Very helpful and useful!
Just a note on network drives – if your data/files happen to be on a network drive, and not on C: or a local drive, then the windows task scheduler may not work properly. The tricky thing is that R is smart enough to realize that “X:” drive is the same as \\company_network\\users_dirs\\X\\, but windows scheduler is not. You might have to change the file paths in your code accordingly. Some folks went through similar pain –
http://windowssecrets.com/forums/showthread.php/161351-Task-scheduler-not-running-my-batch-file
Thanks for the added info and link.
gmailR looks like a great package! Unfortunately, I’m having trouble loading it. I get the following response:
* installing *source* package ‘gmailR’ …
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: no visible binding for ‘<<-' assignment to '.UNAME'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch – i386
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: inDL(x, as.logical(local), as.logical(now), …)
error: unable to load shared object 'C:/Users/Jon.INCUBET/Documents/R/win-library/3.1/rJava/libs/i386/rJava.dll':
LoadLibrary failure: %1 is not a valid Win32 application.
Error : package 'rJava' could not be loaded
Error: loading failed
Execution halted
*** arch – x64
ERROR: loading failed for 'i386'
* removing 'C:/Users/Jon.INCUBET/Documents/R/win-library/3.1/gmailR'
Error : Command failed (1)
Warning message:
In pacman::p_load_gh("trinker/gmailR") :
Failed to install/load:
trinker/gmailR
I think this means that R doesn't know where Java is located. I installed Java, but I am still getting the same error. I tried running loading the rJava package – using library(rJava) – and it loads without any error.
Can you help me?
If you can load rJava this is weird. Please try thsee things:http://trinker.github.io/qdap/vignettes/qdap_vignette.html#install
You can download java for 32 and 64 bit and save both files on your c drive. Then you can tell R where these two files are and gmailR should work. e.g. on your R script write something like:
Sys.setenv(JAVA_HOME=’C:/Program Files/Java/jre1.8.0_31′) # for 64-bit version
Sys.setenv(JAVA_HOME=’C:/Program Files (x86)/Java/jre1.8.0_31′) # for 32-bit version
library(rJava)
This will let R where Java is.
HTH
Hi folks,
Thanks for the great tips. I got stuck so any help would be greatly appreciated! I’ve created the .bat file but when I run it I get the following message:
ARGUMENT ‘BATCH’ __ignored__ and that’s it. The script does not execute. What am I doing wrong? Here is the content of my batch file for reference:
@echo off
“C:\Program Files\R\R-3.1.2\bin\R.exe” BATCH “C:\Users\eyv\Desktop\task\TJ-num-of-items-in-search.R”
I had to type in the full location of the R.exe and the R script as @apwheele said otherwise it did not work at all.
Hi Jordan- I ran into the exact same problem.
Try this using CMD BATCH (your code is just BATCH) and put lines 2 and 3 on the same row.
Your slightly modified example below:
@echo off
“C:\Program Files\R\R-3.1.2\bin\R.exe” CMD BATCH “C:\Users\eyv\Desktop\task\TJ-num-of-items-in-search.R”
Thank you for this video. I have one issue- when I try to run the batch file I get the following error:
“‘R’ is not recognized as internal or external command, operable program or batch file”
Any ideas on how to solve this? Thanks everyone.
Someone asked the same question via email a week back and this helped:
This means R is not on your path. To solve…
gsub("library", "bin", .libPaths())You are the man. Everything looks to be working perfectly. Thanks again for the help! This video is awesome.
Reblogged this on bsbrug <- and commented:
Geração de Gráficos e outras apresentações agendadas.
And what happen if I use RStudio for Windows, what can I have to change? Cause if i just change R.exe by RStudio.exe it dosen´t work
RStudio uses R. It’s an IDE wrapper around R. Find where R is located on your machine and put it on your path. See my comment to Boom above: https://trinkerrstuff.wordpress.com/2015/02/11/scheduling-r-tasks-via-windows-task-scheduler/#comment-1711
Hi Tyler,
Thank you very much for the detailed tutorial. I followed all the steps, including apwheele’s suggestions (added the R.exe path the environmental variables), but when I click on the .bat file, the rompt starts and immediately closes. The script doesn’t execute.
Here is how my .bat file looks like (I created it in .txt file and saved as .bat):
@echo off
“C:\Program Files\R\R-3.2.0\bin\x64\R.exe” CMD BATCH “C:\Users\viola\Documents\Plotly\Scheduled_Script\Sales_Dashboard_Scheduled.R”
My R script starts with this:
setwd(“C:/Users/viola/Documents/Plotly/Scheduled_Script”)
library (RODBC)
library (plyr)
library (ggplot2)
library (shiny)
library (plotly)
library (dplyr)
ch <- odbcConnect("Cumulus_DB_test", believeNRows=FALSE) #connects to the DB and runs SQL query
source("variables.R") #stores my DB connection credentias
source("plotly.R") #stores my Plotly credentials
I store plotly.R & variables.R in the same folder as the main script.
What am I doing wrong? Any advice is much appreciated!
UPDATE: I was able to run it without .bat file directly in Task Scheduler following this instructions – http://stackoverflow.com/questions/2793389/scheduling-r-script
Why .bat file doesn’t run the script?
Nice find 🙂
I’m unsure why your bat file didn’t run but what did the output file from R look like, the R.out? If that’s not there then R didn’t even run and the .bat file is set up wrong.
Hi Tyler,
I have an R code that does something and then sends an email to a list of recipients when the code has run.
When run on Rstudio – the code runs successfully (i.e. all the necessary files are created) AND emails are sent out successfully.
When run via Windows Task Scheduler – the code runs successfully (i.e. all the necessary files are created) BUT emails are not sent out.
I am just not able to figure out why a part of the code is running fine on both Rstudio & via task scheduler, and another part only runs on Rstudio? Following are two pieces of code that I am using to send out emails – both are working fine enough when run on Rstudio.
1.
library(RDCOMClient)
path_name <- file.path(mainDir, subDir)
subject <- paste0("Data quality checks completed for ", analysis_date)
body <- paste0("Data summary has been compiled for all the farms for ", analysis_date,
". All the data summaries are saved in the folder .”)
email_fn <- function(recipient) {
OutApp <- COMCreate("Outlook.Application")
outMail = OutApp$CreateItem(0)
outMail[["To"]] = recipient
outMail[["subject"]] = subject
outMail[["body"]] = body
outMail$Send()
}
#email_fn(recipient = "person1@abc.com")
#email_fn(recipient = "person2@abc.com")
2.
library(sendmailR)
from <- "sender@abc.com"
to <- c("person1@abc.com","person2@abc.com")
subject <- "Email Subject"
body <- "Email body."
mailControl = list(smtpServer = "tucson.websitewelcome.com")
sendmail(from = from, to = to, subject = subject, msg = body, control = mailControl)
Would you know what might be happening here?
Thanks,
Ankur
what does Rout say?
Hi Tyler,
I have the same batch file with RDCOM setup as Ankur, and running into same issue. When the “Run whether user is logged on or not”, my task runs and the output is created, but RDCOM is not sending the email. All runs OK when the box is not ticked… However, I’d like to be able to run tasks even when my computer is logged off.
Any ideas why RDCOM gets stumped by the user context?
Nik
I got this error:
Error in COMCreate(guid, existing = FALSE) :
Failed to create COM object: Server execution failed
Calls: email_fn -> COMCreate -> getCOMInstance -> COMCreate -> .Call
Execution halted
Rout doesn’t print anything for this part of the code. Anyway, figured out the problem. In the task scheduler security options, earlier I had checked “Run whether user is logged on or not”. I un-checked that and checked “Run only when user is logged on” – this did the trick and the emails are now going through. Thanks 🙂
Hi Ankur,
I have tried different options, whether checked “Run whether user is logged on or not” or check “Run only when user is logged on”, both fail to send the email with or without attachment. However, when I run the R code manually without the Task Scheduler, it is able to send the email with or without attachment. So what did I miss out in Task Scheduler, that fail to run my code? My code as below:
analysis_date <- Sys.Date()
subject <- paste0("Historical Data Analysis and Report completed for ", analysis_date)
body <- paste0("Data summary has been compiled for all the farms for ", analysis_date,
". All the data summaries are saved in the folder .")
path_to_attch_file <- paste(getwd(),"/reports/RealTimeUpdate.pdf",sep="")
email_fn <- function(recipient) {
OutApp <- COMCreate("Outlook.Application")
outMail = OutApp$CreateItem(0)
outMail[["To"]] = recipient
outMail[["subject"]] = subject
outMail[["body"]] = body
# outMail[["Attachments"]]$Add(path_to_attch_file)
outMail$Send()
}
email_fn(recipient = "myname@yahoo.com")
> analysis_date subject body path_to_attch_file
> email_fn <- function(recipient) {
+ OutApp email_fn(recipient = “tanthiamhuat@yahoo.com”)
Error in COMCreate(guid, existing = FALSE) :
Failed to create COM object: Access is denied.
Calls: email_fn -> COMCreate -> getCOMInstance -> COMCreate -> .Call
Execution halted
On your path to attach file, change “/” to “\\”. That worked for me.
This was an awesome post! It worked great (with the addition of apwheele’s suggestion).
I’m having a similar problem to Ankur’s above, but I don’t have the option of checking the “Run only when user is logged on” button, as this scheduled task is run on a remote server. The task works as expected when a user is logged in (both scheduled and force-run), but if the user logs out, the task completes, but no email is sent.
Additionally, when I write an error file from this scheduled task, I get the following when the user isn’t logged in:
“”,”x”
“1”,”package or namespace load failed for ‘sendmailR'”
I’ve confirmed that sendmailR is installed in the local library for both the user account that runs the task, as well as the C:\Users\Administrator directory.
Any thoughts on what else to try?
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Thanks for this. Has really helped me build the case for using R at work. Cheers!
Hi Tyler,
I´m a user of some of your packages, I´m from Spain. Thanks.
I´ve a trouble with mi project. In few words, I have a script in R, that scraps the web to get the securities of the spanish values.
I have my script in one hand, my R file, and finally my file .bat to schedule the action.
It doesn´t works, I don´t know why? How can you help me, If you a able to of course.
Thank you very much
Pablo
I´m sure that Im doing a lot of things wrong, so I give you my codes.
RScript
library(httr)
library(XML)
url <- "http://www.infobolsa.es/acciones/ibex35"
doc = htmlParse(url)
tableNodes = getNodeSet(doc, "//table")
ibex35 = readHTMLTable(tableNodes[[1]],encoding="UTF-8",trim = TRUE,as.data.frame = TRUE)
write.csv(ibex35, file = "swirl_temp/ibex35.csv")
print(ibex35)
.bat file
@echo off
R CMD BATCH C:\Users\Pablo Ruigomez\Documents\swirl_temp
.R file
The R Script ^
Thank you again
I used outMail[[“Attachments”]]$Add(“path_to_attach_file”) line of code to add attachment but didn’t work.
Error:Error in outMail[[“DS.xlsx”]] :
Cannot locate 0 name(s) DS..xlsx in COM object (status = -2147352570)
Just to confirm: Is “path_to_attach_file” the current directory?
Thanks in advance,
DS
Hello,
Would you please help me to fix this issue:
Rout:
@echo off
Error: unexpected ‘@’ in “@”
Execution halted
What if I want the script corresponding to the .bat file to use variables and functions that belong to the working directory, but are not self-contained within that file? Currently, when I run the bat file, it gives me an error due to the fact that I am calling a function from another script. Yes, I could solve this by placing the fun in the script, but I also need to use global “counter” variables that need to be tracked over time. Thanks for the help!!
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