class(inputR)
[1] "GRanges"
attr(,"package")
[1] "GenomicRanges"
class(chipR)
[1] "GRanges"
attr(,"package")
[1] "GenomicRanges"

raw.output = bayespeak(as(chipR, "RangedData") , as(inputR, "RangedData"))
Error in as.vector(x, mode) : invalid 'mode' argument

Enter a frame number, or 0 to exit   

1: bayespeak(as(chipR, "RangedData"), as(inputR, "RangedData"))
2: strand.split(treatment)
3: as.factor(bed$strand)
4: factor(x)
5: as.vector(exclude, typeof(x))

The problem is in split.strand function. bed$strand is a factor-Rle and as.factor does not work on it:

Browse[4]> bed$strand
factor-Rle of length 6846477 with 2 runs
  Lengths: 3419269 3427208
  Values :       +       -
Levels(3): + - *
Browse[4]> as.factor(bed$strand)
Error during wrapup: invalid 'mode' argument

   sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8   
 [6] LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BayesPeak_1.24.0     GenomicRanges_1.24.2 GenomeInfoDb_1.8.3   IRanges_2.6.1        S4Vectors_0.10.2     BiocGenerics_0.18.0  BiocParallel_1.6.5  
[8] colorout_1.1-0       BiocInstaller_1.22.3

loaded via a namespace (and not attached):
[1] zlibbioc_1.18.0 XVector_0.12.1  tools_3.3.1