[BioC] rtracklayer browserView

[Dan Tenenbaum]

Hi Dave,

----- Original Message -----
> From: "Dave Gerrard" <davetgerrard at gmail.com>
> To: bioconductor at r-project.org
> Sent: Wednesday, June 25, 2014 4:09:41 AM
> Subject: [BioC] rtracklayer browserView
> 
> Hi,
> I wanted to try out UCSC views in rtracklayer but I seem to have
> fallen at
> the first hurdle. I could not get the example code for browserView()
> to
> work and it throws an error I don't understand.  Session info below.
> 
> Looks like I'm the second person to report this problem this year (no
> reply
> to the first)
> https://stat.ethz.ch/pipermail/bioconductor/2014-April/058989.html
> 
> 
> Dave Gerrard
> 
> 
> 
> > require(rtracklayer)
> > session <- browserSession()
> > browserView(session,
> +             GRangesForUCSCGenome("hg19", "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("hg19", "chr2",
> IRanges(20000,
>        50000)))
> 1: browserView(session, GRangesForUCSCGenome("hg19", "chr2",
> IRanges(20000,
>        50000)))
> > sessionInfo()
> R version 3.0.3 (2014-03-06)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> 
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
> Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
> 
> [5] LC_TIME=English_United Kingdom.1252
> 
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets
>  methods
> base
> 
> other attached packages:
> [1] rtracklayer_1.22.5   GenomicRanges_1.14.4 XVector_0.2.0
>  IRanges_1.20.7       BiocGenerics_0.8.0
> 

I suggest that you upgrade to the latest release version of R (3.1.0) and Bioconductor (2.14).

The example works for me on those versions.

Dan



> 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
>  Rsamtools_1.14.3
> [6] stats4_3.0.3      tools_3.0.3       XML_3.98-1.1
>      zlibbioc_1.8.0
> >
> 
> 	[[alternative HTML version deleted]]
> 
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