I'm currently working with the DNaseR package but am having issues performing the footprinting analysis of the DNase Seq data in the specified .bam file. 

 I performed the example code from ?DNaseR as a test and everything worked well: 

> library('DNaseR')

> bamfile <- "chrY_3Kb_wgEncodeUwDgfTh1Aln.bam"

> f <- system.file("extdata", bamfile, package="DNaseR",mustWork= TRUE)

> dgf <- footprints(bam = f, chrN = "chrY", chrL = 3e6, p = 1e-9, width = c(6,40), N=2e6)

To save space, I have omitted the output of  >dgf, but it looked fine. 

Next, I tried to load another file using the following lines:

>setwd('~/Documents/Bam Files')

>bamfile <- '~/Documents/Bam Files/mybamfile.bam'

>bam.fp <- footprints(bam = bamfile, chrN = "chrY", chrL = 1.5e7, p=1e-9, width = c(6,50), N = 1e5)

...And I received the following error: 

Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : 
  subscript contains NAs or out-of-bounds indices

I can't find much information on NSBS or S4Vectors, the package that contains it. As a result I'm not really sure what this error is referring to or how to fix it.

Here's my sessionInfo, in case that helps.

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] DNaseR_1.4.0         IRanges_2.0.1        S4Vectors_0.4.0      BiocGenerics_0.12.1 
[5] BiocInstaller_1.16.1

loaded via a namespace (and not attached):
[1] Biostrings_2.34.1    bitops_1.0-6         GenomeInfoDb_1.2.4   GenomicRanges_1.18.4
[5] Rsamtools_1.18.3     tools_3.1.2          XVector_0.6.0        zlibbioc_1.12.0     

 Thanks in advance for any help with this problem! 

Martin