[BioC] ExomeCopy package error

[nat [guest]]

Hi,
I am testing ExomeCopy on a set of illumina sequencing data generated after agilent custum gene set  capture, only  35 gene exons overall (~ 300 Mb total).
1-My first question would be : is the method reliable for smaller capture?
2-Secondly.,
I sucessfully used  the method on the data provided with the vignette. I then tried with my own set of data
in total 10 samples, across  2282 rows , I have  calculated the GC and bg values nad went on to the next step where I ran exomeCopy on one sample and one chromosome

###this seems to work for certains samples, expect the warning for small subset
> fit <- exomeCopy(rdata["Chr10"], sample.name = exome.samples[10],
+ X.names = c("bg", "GC", "GC.sq", "width"), S = 0:6,
+ d = 2)
Warning message:
In exomeCopy(rdata["Chr10"], sample.name = exome.samples[10], X.names = c("bg",  :
  exomeCopy was tested for thousands of ranges covering a targeted region on a single chromosome.  The results might not be reliable for less than a hundred ranges.


###then I try with another sample and got this error message 
Error in if (goto.cnv < 1/(nstates - 1)) { : 
  missing value where TRUE/FALSE needed

I am not sure where this comes from and would like some help on this

>  fit <- exomeCopy(rdata["Chr10"], sample.name = exome.samples[7],
+ X.names = c("bg", "GC", "GC.sq", "width"), S = 0:6,
+ d = 2)
Error in if (goto.cnv < 1/(nstates - 1)) { : 
  missing value where TRUE/FALSE needed
In addition: Warning message:
In exomeCopy(rdata["Chr10"], sample.name = exome.samples[7], X.names = c("bg",  :
  exomeCopy was tested for thousands of ranges covering a targeted region on a single chromosome.  The results might not be reliable for less than a hundred ranges.
> exome.samples
 [1] "sample9"  "sample8"  "sample7"  "sample6"  "sample5"  "sample1" 
 [7] "sample16" "sample15" "sample14" "sample13"

 
example if my data

#####
RangedData with 2282 rows and 15 value columns across 18 spaces
        space                 ranges   |   sample9   sample8   sample7
     <factor>              <IRanges>   | <integer> <integer> <integer>
1        Chr1 [115247069, 115247168]   |      4369      4446      3675
2        Chr1 [115247169, 115247268]   |      8222      8081      6978
3        Chr1 [115247269, 115247368]   |      9548     10026      8690

 -- output of sessionInfo(): 

R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] exomeCopy_1.2.0      Rsamtools_1.8.6      Biostrings_2.24.1   
[4] GenomicRanges_1.8.13 IRanges_1.14.4       BiocGenerics_0.2.0  

loaded via a namespace (and not attached):
[1] bitops_1.0-4.1 stats4_2.15.0  tools_2.15.0   zlibbioc_1.2.0


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