I would guess you don't have the dependent library active, try adding this on line 6 before it loads the Matrix library as it seems to depend on the methods library:

library (methods);

Sometimes on default, R will load this automatically but in Omniscope you have to make sure you state every library being used. It's probably a similar issue to this:

http://stackoverflow.com/questions/19680462/rscript-does-not-load-methods-package-r-does-why-and-what-are-the-consequen


EDIT: Question for Visokio developers,

Does Omniscope look into R_DEFAULT_PACKAGES and .Rprofiles? If so you follow the post below to have default libraries always being added in Omniscope based on your settings in your own version of R.


http://stackoverflow.com/questions/10300769/how-to-load-packages-in-r-automatically

Hi Martin,

When you output data from R back into Omniscope it needs to be as a data frame. To solve this, replace your output_data line with this:

output_data <- as(rules,"data.frame")

Hope this helps,

Glen

Daniel,

Your idea about R default packages is a great one, I'll try to get it implemented by next week.

Dan

Thanks Dan and Glen,

The data.frame was the issue.

Martin