[BioC] Help with error when trying to run browserView from rtracklayer

John Brothers [guest] guest at bioconductor.org
Tue Apr 15 18:27:30 CEST 2014

I have noticed an error while using another package when it was trying to open a browser and view custom tracks in UCSC genome. I decided to just see if I could run a simple browserView() directly in a new R session and I still seem to have an error. Any idea what might be going on?

Here is my code followed by an error and a traceback()

> library(rtracklayer)
> session <- browserSession()
> browserView(session, GRangesForUCSCGenome(genome="hg19, chrom="chr2", IRanges(20000, 50000)))

Warning message:
In .local(object, range, track, ...) : NAs introduced by coercion

Error in ucscTrackModes(ucscTracks(object)) : error in evaluating the argument 'object' in selecting a method for function 'ucscTrackModes': Error in names(trackIds) <- sub("^ ", "", sapply(nodes, xmlValue)) : attempt to set an attribute on NULL

> traceback()
7: ucscTrackModes(ucscTracks(object))
6: .local(object, ...)
5: ucscTrackModes(view)
4: ucscTrackModes(view)
3: .local(object, range, track, ...)
2: browserView(session, GRangesForUCSCGenome(genome = "hg19", chrom = "chr2",
       IRanges(20000, 50000)))
1: browserView(session, GRangesForUCSCGenome(genome = "hg19", chrom = "chr2",
       IRanges(20000, 50000)))

 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

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

other attached packages:
[1] rtracklayer_1.22.3   GenomicRanges_1.14.4 XVector_0.2.0
[4] IRanges_1.20.6       BiocGenerics_0.8.0

loaded via a namespace (and not attached):
[1] Biostrings_2.30.1 bitops_1.0-6      BSgenome_1.30.0   RCurl_1.95-4.1
[5] Rsamtools_1.14.3  stats4_3.0.2      tools_3.0.2       XML_3.98-1.1
[9] zlibbioc_1.8.0

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