[Bioc-devel] Windows error "UCSC library operation failed" in package karyoploteR

bernat bgel @ending from igtp@c@t
Sun Sep 30 22:44:00 CEST 2018

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


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