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Last seen 10.1 years ago
I went through the rtracklayer vignette and got the following error:
> library('rtracklayer')
> data(targets)
> targetRanges <- IRanges(targets$start,targets$end)
> targetTrack <-with(targets,GRangesForUCSCGenome("hg18",chrom,targetR
anges,strand,name,target))
> subTargetTrack <- targetTrack[1]
> browseGenome(subTargetTrack)
Error in as.vector(x, "character") :
cannot coerce type 'closure' to vector of type 'character'
> traceback()
12: as.character.default(call[[1L]])
11: as.character(call[[1L]])
10: callGeneric()
9: .local(object, range, track, ...)
8: (function (object, range, track, ...)
standardGeneric("browserView"))(<s4 object="" of="" class="" "ucscsession"="">,
<s4 object="" of="" class="" "compressedirangeslist"="">)
7: (function (object, range, track, ...)
standardGeneric("browserView"))(<s4 object="" of="" class="" "ucscsession"="">,
<s4 object="" of="" class="" "compressedirangeslist"="">)
6: do.call(browserView, viewParams)
5: .local(object, ...)
4: browseGenome(as(object, "RangedData"), ...)
3: browseGenome(as(object, "RangedData"), ...)
2: browseGenome(subTargetTrack)
1: browseGenome(subTargetTrack)
Interestingly, the following works as expected:
> browseGenome(subTargetTrack,range=base::range(subTargetTrack))
To me, this seems to be a bug, since the I copied the code from the
vignette and it failed.
Of course, I might just be missing something.
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] rtracklayer_1.22.3 GenomicRanges_1.14.4 XVector_0.2.0
IRanges_1.20.6 BiocGenerics_0.8.0 vimcom_0.9-93
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 stats4_3.0.2 tools_3.0.2
XML_3.98-1.1
[9] zlibbioc_1.8.0
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