rtracklayer\'s browseGenome function failes when invoked according to vignette
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@guest-user-4897
Last seen 9.5 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 -- Sent via the guest posting facility at bioconductor.org.
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@michael-lawrence-3846
Last seen 2.3 years ago
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Good catch. I've fixed it in release (version 1.22.4). This no longer happens in devel since we moved completely to GRanges. The actual error though is a bug in the methods package, and I've submitted a patch here: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15691. Michael On Mon, Feb 24, 2014 at 7:40 AM, Marcel Schilling [guest] < guest@bioconductor.org> wrote: > > 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,targetRanges,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 > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
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