[BioC] IRanges: Error in mk_singleBracketReplacementValue(x, value)

[Nicolas Delhomme]

Hi,

I'm currently investigating this error:

Error in mk_singleBracketReplacementValue(x, value) 

that was reported to me there: http://permalink.gmane.org/gmane.sci...onductor/43677.

Following the traceback:

1: easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", annotationMetho
 2: easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", annotationMetho
 3: parallelize(obj = filesList, fun = .doCount, nnodes = nbCore, rnaSeq = obj,
 4: parallelize(obj = filesList, fun = .doCount, nnodes = nbCore, rnaSeq = obj,
 5: parallelize(obj, fun, nnodes, ...)
 6: parallelize(obj, fun, nnodes, ...)
 7: .parallelize(obj, fun, nnodes, ...)
 8: lapply(obj, fun, ...)
 9: lapply(obj, fun, ...)
10: FUN(X[[1]], ...)
11: fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter
12: fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter
13: coverage(aln.info$rng.list[match(valid.names, names(aln.info$rng.list))], w
14: coverage(aln.info$rng.list[match(valid.names, names(aln.info$rng.list))], w
15: .local(x, shift, width, weight, ...)
16: normarg_for_multiple_coverage(weight, "weight", x_len, names(x), 1)
17: `[<-`(`*tmp*`, arg2ref, value = <S4 object of class "CompressedNumericList"
18: `[<-`(`*tmp*`, arg2ref, value = <S4 object of class "CompressedNumericList"
19: mk_singleBracketReplacementValue(x, value)

lead me to the IRanges:::normarg_for_multiple_coverage function, where the origin of this error is located. I can however not easily track it further down. I have attached a rda file that contains the environment of that function call.

Running the following reproduces the error:

library(IRanges)
load("data-to-reproduce-error.rda")
arg2[arg2ref] <- arg

Any help would be greatly appreciated :-)

My sessionInfo()

R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] IRanges_1.15.44    BiocGenerics_0.3.2

loaded via a namespace (and not attached):
[1] stats4_2.15.1

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
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