Archive for September, 2014

Error notifications from R

4 Sep 2014

I’m enthusiastic about having R notify me when my script is done.

But among my early uses of this, my script threw an error, and I never got a text or pushbullet about that. And really, I’m even more interested in being notified about such errors than anything else.

It’s relatively easy to get notified of errors. At the top of your script, include code like options(error = function() { } )

Fill in the function with your notification code. If there’s an error, the error message will be printed and then that function will be called. (And then the script will halt.)

You can use geterrmessage() to grab the error message to include in your notification.

For example, if you want to use RPushbullet for the notification, you could put, at the top of your script, something like this:

options(error = function() { 
                    library(RPushbullet)
                    pbPost("note", "Error", geterrmessage())
                })

Then if the script gives an error, you’ll get a note with title “Error” and with the error message as the body of the note.

Update: I knew I’d heard about this sort of thing somewhere, but I couldn’t remember where. Duh; Rasmus mentioned it on twitter just a couple of days ago! Fortunately, he reminded me of that in the comments below.

Another update: Ian Kyle pointed out in the comments that the above function, if used in a script run with R CMD BATCH, won’t actually halt the script. The simplest solution is to add stop(geterrmessage()), like this:

options(error = function() { 
                    library(RPushbullet)
                    pbPost("note", "Error", geterrmessage())
                    if(!interactive()) stop(geterrmessage())
                })

Notifications from R

3 Sep 2014

You just sent a long R job running. How to know when it’s done? Have it notify you by beeping, sending you a text, or sending you a notification via pushbullet.

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