[BioC] MEDIPS error extending reads

[Stephen Turner]

Lukas (and others):

I'm using the new version of MEDIPS (1.10.0) and I'm getting an error
when trying to use MEDIPS.createSet():

MEDIPS.createSet(file="myalnment.bam",
BSgenome="BSgenome.Mmusculus.UCSC.mm9", extend=300, shift=0, uniq=T,
window_size=100)

Here's the error I get:

Reading bam alignment myalnment.bam
Total number of imported short reads: 6150717
Extending reads...
Error in regions$stop[regions$strand == "+"] = regions$stop[regions$strand ==  :
  NAs are not allowed in subscripted assignments

Not sure what to do here. Thanks for any help.

Stephen

> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
[1] BSgenome.Mmusculus.UCSC.mm9_1.3.19 MEDIPS_1.10.0
[3] DNAcopy_1.34.0                     BSgenome_1.28.0
[5] Biostrings_2.28.0                  GenomicRanges_1.12.1
[7] IRanges_1.18.0                     BiocGenerics_0.6.0
[9] BiocInstaller_1.10.0

loaded via a namespace (and not attached):
[1] RCurl_1.95-4.1   Rsamtools_1.12.0 XML_3.96-1.1     biomaRt_2.16.0
[5] bitops_1.0-5     gtools_2.7.1     stats4_3.0.0     tools_3.0.0
[9] zlibbioc_1.6.0