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!
Related
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.
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.
I want to run an R script (in Win 7) from SQL Server 2014 each time a new record is added (to perform some analysis on the data). I saw that this can be done with the xp_cmdshell command which is like running it manually from the command line.
My problems (and questions) are:
I've made out from various websites that probably the best option is to use Rscript. This would have to be used at the command line as:
C:\Program Files\R\R-3.2.3\bin\x64\Rscript "my_file_folder\my_file.r
Can I copy Rscript.exe to the folder where my script is, such that I can run my script independently, even if R is not installed? What other files do I need to copy together with Rscript.exe such that it would work independently?
My script loads some packages that contain functions that it uses. Is there a way to somehow include these in the script such that they don't have to be loaded every time (it takes about 5 sec so far and I need this script to be faster)? Or is there a way to only load these packages the first time that the script runs?
In case the overall approach I've described here is not the best one, I am open to doing it differently. Maybe there is a way to somehow package the R script together with all the required dependencies (libraries and other parts of the R software which the script would need to run independently).
What I ultimately need is a for the script to run silently, and reasonably fast, without any windows or anything else popping up, each time a new record is added to my database, do the analysis and exit.
Thanks in advance for any answers.
UPDATE:
I figured out an elegant solution to running the R script. I'm setting up a job in SQL Server and inside that job I'm using "xp_cmdshell" to run my script as a parameter to Rscript.exe, as detailed at point 1 above. I can start this job from any stored procedure and the beauty of it is that the stored procedure does not wait for the script to finish. It just triggers the job (that runs the script in a separate thread) and then it continues with its business.
But questions from points 1 and 2 still remain.
I have a cron job that launches an Rscript to go fetch some data and stash it away in a database. Sometimes the source isn't ready so it waits. Sometimes the source skips a data point so the script ends up waiting until another instance is started from cron. Now that two instances are running they cause problems with each other. Is there something like the following pseudo code that I could put at the top of my scripts so they stop when they see another instance of themselves is already running:
stopifnot(Sys.running('nameofscript.r'))
One thing I thought to do would be for the script to make a temp file with a fixed name at the start and then delete that temp file at the end. This way the script can check for the existence of the file to know if it's already running. I also see there's something called flock which is probably a better solution than that but I'd prefer if there was a way R can do it without bash commands (I've never really learned any bash). If there isn't a pure R way to do this, can the R script call flock on itself or would it only work if the cron task calls a bash script that then calls the rscript. If it isn't already obvious, I don't really know how to use flock.
I usually open the R console all day long, but sometimes I need to clean my history and my workspace's background so that I can test functions or load new data.
I'm wondering whether there is an easier way to use a command line in .Rprofile so that I can refresh the R console without quitting or rebooting my current session.
What I have usually done for this is to q() without saving and then start R again and clean the History. I think somebody here might be able to give me some better suggestions.
Thanks in advance.
For what concerns history, in UNIX-like systems (mine is Debian) this command refreshes it
loadhistory("")
However, as said in comments, loadhistory seems to be platform-dependent.
Check your ?loadhistory if present on your platform. Mine says:
There are several history mechanisms available for the different
R consoles, which work in similar but not identical ways. There
are separate versions of this help file for Unix and Windows.
The functions described here work on Unix-alikes under the
readline command-line interface but may not otherwise (for
example, in batch use or in an embedded application)