Search
Question: rtracklayer\'s browseGenome function failes when invoked according to vignette
0
gravatar for Guest User
3.8 years ago by
Guest User12k
Guest User12k 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,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.
ADD COMMENTlink modified 3.7 years ago by Michael Lawrence9.8k • written 3.8 years ago by Guest User12k
0
gravatar for Michael Lawrence
3.7 years ago by
United States
Michael Lawrence9.8k wrote:
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]]
ADD COMMENTlink written 3.7 years ago by Michael Lawrence9.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 109 users visited in the last hour