[BioC] error in calculate integer copy numbers. bug?

[Johnbosco [guest]]

I used getSegmentReadCountsFromBAM() to get a GRanges object from a list of tumor-normal bam files
Then I used referencecn.mops(). Whenever I try to calculate integer copy numbers using calcIntegerCopyNumbers() I get an error. This error can be reproduced using the data provided by cn.mops so this might be a bug? 

>data(cn.mops)
>resRef2 <- referencecn.mops (XRanges[,1], XRanges[,2])
Normalizing...
Starting local modeling, please be patient...
Reference sequence:  chrA
Starting segmentation algorithm...
Using "fastseg" for segmentation.
> resRef5 <- calcIntegerCopyNumbers(resRef2)
Error in `colnames<-`(`*tmp*`, value = "S_1") :
  length of 'dimnames' [2] not equal to array extent 

 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: x86_64-redhat-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] snow_0.3-13          cn.mops_1.8.3        GenomicRanges_1.14.4
[4] XVector_0.2.0        IRanges_1.20.6       Biobase_2.22.0      
[7] BiocGenerics_0.8.0   BiocInstaller_1.12.0

loaded via a namespace (and not attached):
[1] Biostrings_2.30.1 bitops_1.0-6      Rsamtools_1.14.2  stats4_3.0.2     
[5] tools_3.0.2       zlibbioc_1.8.0 

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