I have written a series of R Scripts that create csv files. From there, Tableau will read the csv's and update various dashboards. As Tableau can easily be scheduled to update on a daily cadence, I was hoping to do the same with my R Script.
While there are a bunch of answers already with solutions for Windows, there hasn't been a solution posted for OSX. I have looked into trying to run my script in Terminal and use automator to do it, but couldn't quite figure it out. Basically, when the shell script runs it terminates midway through because there are errors in the R Script - but I do not care about the errors. The Automator didn't work as well.
Additionally, I also looked into Data Integration/Pentaho but the additional software configuration and subsequent installation seemed difficult.
Any help or insight would be greatly appreciated! Thanks!
Type crontab -e and add this line to the resulting file
#daily Rscript 1.R && Rscript 2.R
It will run the files 1.R, followed by 2.R at midnight every day. Hope that helps.
The most flexible way to do this is to use launchd, the service that manages processes on OS X. You can look at some examples in the official documentation.
Related
I have two different versions of R installed, one which is up to date and which I use for all my regular R coding (needs to be up to date so that I can use various updated and new packages) and one which I use to access OLAP cubes (needs to be the R Client from Microsoft, because this is the only one which supports the olapR package, and which currently uses R version 3.4.3).
Since, in theory, I only have to access the OLAP cube once a month, I "outsourced" this task to a different RStudio project, in which I download and save the required data for all other projects. Hence, all other projects never require the olapR package to be installed and can and will be run in the up to date R version.
Now, ideally I would like to link my R version to my projects, so that I do not have to change my global R version and restart RStudio every time I access the OLAP cube or work on this data retrieval project (and then switch it back). However, I could not find any options in RStudio to achieve this result.
There are a few threads out there describing the same problem, but with no satisfactory answer in my opinion:
https://support.rstudio.com/hc/en-us/community/posts/200657296-Link-Project-and-R-Version
Rstudio project using different version of R
I also tried looking for a different package than olapR but with similar functionality, but could not find anything except X4R, which seems outdated and does not work for me (https://github.com/overcoil/X4R). Sadly, I am also unable to directly access the databases which the OLAP cube uses for its results, so I cannot go "around" it.
I am happy for any help or suggestions you can offer, whether it is a general workaround to link a project to a specific R version or the (less helpful for the community) solution of accessing the OLAP cube in a different way.
Thanks in advance!
Using the answer from MrGumble I created a .bat file that will execute my .R file using the desired R installation. Even though it is not the answer I thought I would get, I think it is an even better solution to the problem.
For all facing a similar issue, here is the .bat file (never created one before, so also had to google how to do it and I guess some might be in the same position):
#echo off
title Getting data for further processing in R
echo Retrieving OLAP data
echo.
"C:\Program Files\Microsoft\R Client\R_SERVER\bin\Rscript.exe" "C:\Users\me\Documents\Projects\!Data\script.R"
echo.
echo Saved data
echo.
pause
Thanks again to MrGumble for his help.
Skip RStudio.
RStudio is really just an editor (albeit powerful and useful) editor, which starts an R console for you (and the surrounding PATH variables, library locations, etc.).
If your monthly task only requires you to run the R-script (or a bit of interactive work), you can simply execute your preferred version of R from the command line and have it run your R script. E.g.
C:\Users\me>"C:\Program Files (x64)\Microsoft R\bin\Rscript" myscript.R
You might have to define some PATH variables so that the older R doesn't look for packages in the newer R's libraries, but that depends entirely on your current setup.
I have an R script that has been running for a couple of days. I need to change something there but don't want to lose the calculations that have already been done. Is there a way to attach to it and pause and debug? Like with gdb you can attach to an already running process.
I'm sorry to say that there is not. Not given that the script is already running.
Some extra info that won't make you feel better:
You shouldn't write scripts that have to run for days (at least in R), at least not without having them write out RDS files to save your progress.
You could've set up debugging in RStudio before you ran the script.
If you were running Rcpp code you could've used gdb with it (more info from Hadley Wickam's site here).
You can learn more about debugging R code here.
So I wrote my father a neat little R script that pulls financial indicators on stocks, and outputs the info to a csv...
I would like to have it set up so that the script will run automatically once a day, skipping the weekends if possible. I looked around for awhile online and it seems as though the Mac "Automator" App is what I'm looking for.
However, after reading many guides and posts (like this one https://www.r-bloggers.com/how-to-source-an-r-script-automatically-on-a-mac-using-automator-and-ical/) I cannot get it to work...
In trying to replicate what this man did above I get the error that the first path is a directory; while the latter returns stuff like "cat: Rscript: No such file or directory"
So I was wondering if anyone could recommend either any good free software that will allow me to do what I would like, or how to run an R script from the /bin/bash shell
EDIT:
The suggested solution isn't really answering my problem. The issue is making this as easy as possibly for my dad to run, that way he doesn't have to do anything, specifically use the terminal. Ideally I could just schedule a task that repeats every morning, but the cronR package requires Daemon, and the others are just command line tools
I had a similar experience.
I created an automator calendar alarm
added a Execute AppleScript Action and used the following code:
on run {input, parameters}
try
tell application "R"
activate
with timeout of 90000 seconds
cmd "source(\"Dropbox/RScripts/CV19/liibre_coronabr.R\")"
end timeout
end tell
end try
return input
end run
When you save it, just choose the date and time for it to run and select the option to repeat everyday
That's it!
I have a script in R that is frequently called during the day (by other scripts). I call R in a terminal using
Rscript code.R
I notice it takes a lot of time to load packages and set up R.
Is it possible to run R as a background service which I hit using a port or something?
Yes, look into RServe which has been available for over a dozen years for this reason. There are a couple of fairly high profile applications too.
You can check out this add-in for Rstudio, it is not a port like solution but maybe it can help you https://github.com/bnosac/taskscheduleR
I've found a lot of answers on how to run R from a Batch file, but nothing about running a Batch File from R. I know one way to do this is to use system, system2 or shell, but these methods wait for process in the Windows Command Prompt to finish before R accepts another input. I want to run a Batch File which calls a console application that runs indefinitely, and then allow R to do other things. Any help would be greatly appreciated.
The help page ?shell says how to do it. Just run
shell("MyScript.bat", wait=FALSE)