[BioC] RleList

[Massimo Petretich]

Dear All,

I am a hard time converting a list of Rle to a RleList.
The very same code was working fine with R 2.15.2 and IRanges 1.17.1.



> BAM<-readAligned(dirPath=directory, pattern=paste("srtRmdup_",tag, 
> ".bam",sep=""), type="BAM")

> lc <- BAM[ !is.na(chromosome(BAM))]

> cvg <- coverage(lc, extend=eval(parse(text=paste(fragmentSize,"L", 
> sep="")))-width(lc))

> y<-mclapply(cvg[sapply(cvg, length)>3*window], smoothRle, 
> window=window, resolution=resolution, mc.cores=cores)

> head(y,2)
$chr1
numeric-Rle of length 197195000 with 191252 runs
   Lengths:          2990000             1000 ...            10000
   Values :                0 35.7142857142857 ... 1068.71428571429

$chr2
numeric-Rle of length 181748000 with 178193 runs
   Lengths:          2990000             1000 ...            11000
   Values :                0 15.3809523809524 ... 1286.85714285714

> y<-RleList(y)
Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = 
"IRanges") :
integer overflow while summing elements in 'lengths'



# It gives the same error if I convert an RleList to list and then back 
to RleList:


> cvg
RleList of length 35
$chr1
integer-Rle of length 197195057 with 2181706 runs
   Lengths: 3000467       2      27     221 ...      98      21     400   
   250
   Values :       0       1       2       3 ...       2       1       0   
     1

$chr2
integer-Rle of length 181748164 with 2182776 runs
   Lengths: 3000128     250     549      99 ...      51       9      48   
    54
   Values :       0       1       0       1 ...       4       3       2   
     1

$chr3
integer-Rle of length 159599909 with 1760167 runs
   Lengths: 2999875     250       6     123 ...      22     136     114   
   136
   Values :       0       1       0       1 ...       0       1       2   
     1

$chr4
integer-Rle of length 155630246 with 1888170 runs
   Lengths: 3000290     250     229     250 ...       5      92     111   
    47
   Values :       0       1       0       1 ...       2       3       2   
     1

$chr5
integer-Rle of length 152537402 with 1759560 runs
   Lengths: 2999987     250     490     196 ...       9     133      14   
     8
   Values :       0       1       0       1 ...       4       3       2   
     1
...
<30 more elements>


> cvgLst <- as.list(cvg)

> cvg <- RleList(cvgLst)
Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = 
"IRanges") :
integer overflow while summing elements in 'lengths'


# The problem isn't likely the data itself or the syntax,
> cvg<-RleList(cvgLst[1:10])

> cvg
RleList of length 10
$chr1
integer-Rle of length 197195057 with 2181706 runs
   Lengths: 3000467       2      27     221 ...      98      21     400   
   250
   Values :       0       1       2       3 ...       2       1       0   
     1

$chr2
integer-Rle of length 181748164 with 2182776 runs
   Lengths: 3000128     250     549      99 ...      51       9      48   
    54
   Values :       0       1       0       1 ...       4       3       2   
     1

$chr3
integer-Rle of length 159599909 with 1760167 runs
   Lengths: 2999875     250       6     123 ...      22     136     114   
   136
   Values :       0       1       0       1 ...       0       1       2   
     1

$chr4
integer-Rle of length 155630246 with 1888170 runs
   Lengths: 3000290     250     229     250 ...       5      92     111   
    47
   Values :       0       1       0       1 ...       2       3       2   
     1

$chr5
integer-Rle of length 152537402 with 1759560 runs
   Lengths: 2999987     250     490     196 ...       9     133      14   
     8
   Values :       0       1       0       1 ...       4       3       2   
     1
...
<5 more elements>


> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-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] MALDIquant_1.8       rtracklayer_1.22.0   ShortRead_1.20.0
[4] Rsamtools_1.14.2     lattice_0.20-24      Biostrings_2.30.1
[7] GenomicRanges_1.14.4 XVector_0.2.0        IRanges_1.20.6
[10] BiocGenerics_0.8.0

loaded via a namespace (and not attached):
[1] Biobase_2.22.0      bitops_1.0-6        BSgenome_1.30.0
[4] grid_3.0.2          hwriter_1.3         latticeExtra_0.6-26
[7] RColorBrewer_1.0-5  RCurl_1.95-4.1      stats4_3.0.2
[10] tools_3.0.2        XML_3.98-1.1        zlibbioc_1.8.0




Perhaps I am unaware of some changes introduced in the latest version of 
IRanges
that make this operation not possible,
I hope somebody has some suggestions to give me.

Thanks and best regards,
Massimo