I'm not sure what's going on. The examples in my documentation seem to run okay, then I get a weird error at the end apparently outside of my code. I thought something about the example itself could have been messing things up, but as you can see, the error persists even with a commented-out example. I have previously tried commenting out the only part of my examples that ever use graphics, and that didn't fix the problem either. Does anyone have any idea what the problem could be?

Here's the Travis log with the problem: https://travis-ci.org/kjohnsen/MMAPPR2/builds/437132158

Running examples in ‘MMAPPR2-Ex.R’ failed
The error most likely occurred in:
> ### Name: prePeak
> ### Title: Identify chromosomes containing peaks
> ### Aliases: prePeak
> 
> ### ** Examples
> 
> # postPrePeakMD <- prePeak(postLoessMD)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  422.32 24.256 474.836 0.008 0.128 
> grDevices::dev.off()
Error in grDevices::dev.off() : 
  cannot shut down device 1 (the null device)

After some investigation, I discovered that my examples that interacted with graphics did cause the problem. I edited those parts out of the examples (I missed one place when I tried this the first time) and it worked. I guess this is a problem with R itself--my function calls graphics.off() to clean up after itself after writing PDFs and such, and I suppose R, ignorant of the fact, thought it still needed to call dev.off().