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

2018-10-01 Thread Bernat Gel Moreno 
Ops, ok, thanks. Should have reread the documentation.

Thanks

Bernat


El 01/10/2018 a las 2:00, Dario Strbenac escribió:
> Good day,
>
> The import of BigWig files does not work on Windows and is documented. 
> Execute ?BigWigFile-class and notice in the Description section: "These 
> functions do not work on Windows.".
> --
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

2018-09-30 Thread Dario Strbenac 
Good day,

The import of BigWig files does not work on Windows and is documented. Execute 
?BigWigFile-class and notice in the Description section: "These functions do 
not work on Windows.".
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

2018-09-30 Thread bernat 
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


[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel