I am attempting to use BayesPeak. I have a file of mapped reads from a ChIP-seq experiment and from a negative control in bed6 format. 

The following is my output: 

library(BayesPeak)
> raw.output <- bayespeak("chip.bed", "negative.bed", chr = "chr", start = 80000, end = 100000, job.size = 1000)
Read 23148733 records
Read 21898540 records
[0% done] Starting chr:80000-1e+05:Error in var(tr$"+"$norm[x[1]:x[2]]) : 
  error in evaluating the argument 'x' in selecting a method for function 'var': Error in tr$"+"$norm[x[1]:x[2]] : 
  only 0's may be mixed with negative subscripts

I am not sure what is causing this error. Does anyone have some insight into this? I have pasted my session info below.

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] BayesPeak_1.12.0   IRanges_1.20.4     BiocGenerics_0.8.0

loaded via a namespace (and not attached):
[1] stats4_3.0.2