Hi
I got an error message when trying to read bam files (genomicAlignments 1.10).
I even got this error when trying to run the provided examples.
Follows: example code, traceback and sessionInfo
Thanks in advance for any help.
Ariel
> example(readGAlignments)
rdGAlg> ## ---------------------------------------------------------------------
rdGAlg> ## A. readGAlignments()
rdGAlg> ## ---------------------------------------------------------------------
rdGAlg>
rdGAlg> ## Simple use:
rdGAlg> bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",
rdGAlg+ mustWork=TRUE)
rdGAlg> gal1 <- readGAlignments(bamfile)
Error in as.vector(x, mode) :
'.SigArgs' is shorter than '.SigLength' says it should be
------------------------------------------------------------------------------------------------
> traceback()
24: as.vector(x, mode)
23: as.vector(x, mode = "integer")
22: .local(x, ...)
21: as.integer(seqnames(x))
20: as.integer(seqnames(x))
19: get_out_of_bound_index(x)
18: GenomicRanges:::valid.GenomicRanges.seqinfo(x)
17: valid.func(object)
16: validityMethod(object)
15: anyStrings(validityMethod(object))
14: validObject(.Object)
13: initialize(value, ...)
12: initialize(value, ...)
11: new("GAlignments", NAMES = names, seqnames = seqnames, start = pos,
cigar = cigar, strand = strand, elementMetadata = elementMetadata,
seqinfo = seqinfo)
10: GAlignments(seqnames = bamcols$rname, pos = bamcols$pos, cigar = bamcols$cigar,
strand = bamcols$strand, seqlengths = seqlengths)
9: readGAlignments(bam, character(0), use.names = use.names, param = param,
with.which_label = with.which_label)
8: readGAlignments(bam, character(0), use.names = use.names, param = param,
with.which_label = with.which_label)
7: readGAlignments(bamfile)
6: readGAlignments(bamfile) at Rex5e07f874d38#21
5: eval(expr, envir, enclos)
4: eval(ei, envir)
3: withVisible(eval(ei, envir))
2: source(tf, local, echo = echo, prompt.echo = paste0(prompt.prefix,
getOption("prompt")), continue.echo = paste0(prompt.prefix,
getOption("continue")), verbose = verbose, max.deparse.length = Inf,
encoding = "UTF-8", skip.echo = skips, keep.source = TRUE)
1: example(readGAlignments)
------------------------------------------------------------------------------------------------
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)
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] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicAlignments_1.10.0 Rsamtools_1.26.1
[3] Biostrings_2.42.1 XVector_0.14.0
[5] SummarizedExperiment_1.4.0 Biobase_2.34.0
[7] GenomicRanges_1.26.2 GenomeInfoDb_1.10.2
[9] IRanges_2.8.1 S4Vectors_0.12.1
[11] BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] lattice_0.20-29 bitops_1.0-6 grid_3.3.2 zlibbioc_1.20.0
[5] Matrix_1.1-4 BiocParallel_1.8.1 tools_3.3.2
