[BioC] htSeqTools errors

[Juan L. Mateo]

Hi all,

I am trying to use htSeqTools to analyse some ChIP-seq samples and I am 
getting errors on the methods cmds and giniCoverage. Below I paste the 
output of a session.

Any help will be greatly appreciated.


 > what=c("rname", "strand", "pos", "qwidth")
 > param=ScanBamParam(what = what)
 >
 > Con_input<-scanBam('Con_input.fastq.bam', param=param)[[1]]
 > 
Con_input.reads<-GRanges(seqnames=Rle(Con_input$rname),ranges=IRanges(Con_input$pos, 
width=Con_input$qwidth))
 > samples<-RangedDataList(Con_input=as(Con_input.reads,"RangedData"))
 > cmds1<-cmds(samples,k=2)
Computing coverage...
Computing correlations...
Error in d[[i]] : subscript out of bounds
 > ssdCoverage(samples)
Con_input
0.2551517
 > giniCoverage(samples,mc.cores=1)
Simulating uniformily distributed data
Error in sample.int(chrLen[i], as.integer(chrReads[i]), replace = T) :
   invalid 'size' argument
In addition: Warning messages:
1: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf
2: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf
3: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf
4: In eval(expr, envir, enclos) : NAs introduced by coercion




 > sessionInfo()
R Under development (unstable) (2012-02-13 r58337)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_GB       LC_NUMERIC=C         LC_TIME=en_GB
  [4] LC_COLLATE=en_GB     LC_MONETARY=en_GB    LC_MESSAGES=en_GB
  [7] LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_GB LC_IDENTIFICATION=C

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

other attached packages:
[1] htSeqTools_1.1.2     BSgenome_1.23.2      MASS_7.3-17
[4] Biobase_2.15.3       Rsamtools_1.7.33     Biostrings_2.23.6
[7] GenomicRanges_1.7.24 IRanges_1.13.24      BiocGenerics_0.1.4

loaded via a namespace (and not attached):
[1] bitops_1.0-4.1 zlibbioc_1.1.1


-- 
=============================
Juan L. Mateo PhD.
Centre for Organismal Studies (COS) - University of Heidelberg
Im Neuenheimer Feld 230
69120 Heidelberg, Germany
Tel: 0049 (0)6221 54 6493
Fax: 0049 (0)6221 54 5639