[BioC] error in exomeCopy - IRanges?

Lescai, Francesco f.lescai at ucl.ac.uk
Tue Aug 7 00:11:19 CEST 2012

Hi there,
I'm having an error in exomeCopy when I count the CNVs.
No previous error in any of the other steps illustrated in the vignette

the computation of the fit list didn't give any warning and it seems to be formatted correctly 

> fit.list[[1]][1]

ExomeCopy object
sample name: UCLG_502_ATCACG_L003
percent normal state: 79.87%

> summary(fit.list$UCLG_502_ATCACG_L003$`1`)
   Length     Class      Mode 
        1 ExomeCopy        S4 

but then I get

> compiled.segments <- compileCopyCountSegments(fit.list)
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  solving row 1: negative widths are not allowed
Calls: compileCopyCountSegments ... RangedData -> is -> IRanges -> solveUserSEW0 -> .Call2 -> .Call
Execution halted

any idea is much appreciated.

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

 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C                  
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915    
 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915   
 [7] LC_PAPER=C                     LC_NAME=C                     
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C                
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C           

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

other attached packages:
[1] exomeCopy_1.2.0     Rsamtools_1.8.5     Biostrings_2.24.1  
[4] GenomicRanges_1.8.7 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  zlibbioc_1.2.0

More information about the Bioconductor mailing list