Hi all,
I've got a windows only error in one example of one of my packages
(karyoploteR).
The erroring function uses rtracklayer::import to load some data from a BigWig
file with
wig.data <- rtracklayer::import(data, format = "bigWig",
selection=plot.region[i])
where plot.region[i] is a GRanges.
The example used to use the example BigWig file from rtracklayer, but I changed
it to
my own file to see if the problem was with the file itself. The error is
exactly the same
with both files.
From the error text I assume the problem might be related to reading
the data, is it correct?
Any idea of what might be failing?
This is the code of the example producing the error.
> bigwig.file <- system.file("extdata", "BRCA.genes.hg19.bw", package =
> "karyoploteR")
> brca.genes.file <- system.file("extdata", "BRCA.genes.hg19.txt", package =
> "karyoploteR")
> brca.genes <- toGRanges(brca.genes.file)
> seqlevelsStyle(brca.genes) <- "UCSC"
>
> kp <- plotKaryotype(zoom = brca.genes[1])
> kp <- kpPlotBigWig(kp, data=bigwig.file, r0=0, r1=0.3)
Warning in .local(object, ...) :
Invalid argument
lseek(6, 232, invalid 'whence' value (4096)) failed
Error in .local(object, ...) : UCSC library operation failed
Calls: kpPlotBigWig ... mcols -> unlist -> summary -> summary -> .local -> .Call
Execution halted
Thanks a lot
Bernat
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