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Question: rtracklayer 1.6: invalid class "ucscCart" object
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gravatar for Paul Shannon
7.6 years ago by
Paul Shannon1.1k
Paul Shannon1.1k wrote:
Dear Bioc, Following the rtracklayer documentation, section 2.2.4, 'A Shortcut', I encounter the following error > browseGenome (subTargetTrack) Error in validObject(.Object) : invalid class "ucscCart" object: superclass "ANYTHING" not defined in the environment of the object's class > traceback () 13: stop(msg, " ", errors, domain = NA) 12: validObject(.Object) 11: initialize(value, ...) 10: initialize(value, ...) 9: new("ucscCart", vals) 8: .local(object, ...) 7: ucscCart(x) 6: ucscCart(x) 5: range(<s4 object="" of="" class="" "ucscsession"="">, na.rm = FALSE) 4: mergeRange(range(session), range) 3: .local(object, ...) 2: browseGenome(subTargetTrack) 1: browseGenome(subTargetTrack) > summary (subTargetTrack) Length Class Mode 23 RangedData S4 > sessionInfo () R version 2.10.1 (2009-12-14) x86_64-apple-darwin9.8.0 locale: [1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.6.0 microRNA_1.4.0 Rlibstree_0.3-2 Biostrings_2.14.12 IRanges_1.4.8 limma_3.2.1 genefilter_1.28.2 [8] humanStemCell_0.2.3 hgu133plus2.db_2.3.5 org.Hs.eg.db_2.3.6 RSQLite_0.7-3 DBI_0.2-4 AnnotationDbi_1.8.0 Biobase_2.6.1 [15] RCurl_1.2-0 bitops_1.0-4.1 RUnit_0.4.22 loaded via a namespace (and not attached): [1] annotate_1.24.1 BSgenome_1.14.2 splines_2.10.1 survival_2.35-8 tools_2.10.1 XML_2.6-0 xtable_1.5-6
ADD COMMENTlink modified 7.6 years ago by Michael Lawrence9.8k • written 7.6 years ago by Paul Shannon1.1k
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gravatar for Michael Lawrence
7.6 years ago by
United States
Michael Lawrence9.8k wrote:
This sounds like you need to reinstall rtracklayer and/or one of its dependencies. Michael On Thu, Apr 8, 2010 at 8:15 PM, Paul Shannon <pshannon@systemsbiology.org>wrote: > Dear Bioc, > > Following the rtracklayer documentation, section 2.2.4, 'A Shortcut', I > encounter the following error > > > browseGenome (subTargetTrack) > Error in validObject(.Object) : > invalid class "ucscCart" object: superclass "ANYTHING" not defined in the > environment of the object's class > > > traceback () > 13: stop(msg, " ", errors, domain = NA) > 12: validObject(.Object) > 11: initialize(value, ...) > 10: initialize(value, ...) > 9: new("ucscCart", vals) > 8: .local(object, ...) > 7: ucscCart(x) > 6: ucscCart(x) > 5: range(<s4 object="" of="" class="" "ucscsession"="">, na.rm = FALSE) > 4: mergeRange(range(session), range) > 3: .local(object, ...) > 2: browseGenome(subTargetTrack) > 1: browseGenome(subTargetTrack) > > > summary (subTargetTrack) > Length Class Mode > 23 RangedData S4 > > > sessionInfo () > R version 2.10.1 (2009-12-14) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.6.0 microRNA_1.4.0 Rlibstree_0.3-2 > Biostrings_2.14.12 IRanges_1.4.8 limma_3.2.1 > genefilter_1.28.2 > [8] humanStemCell_0.2.3 hgu133plus2.db_2.3.5 org.Hs.eg.db_2.3.6 > RSQLite_0.7-3 DBI_0.2-4 AnnotationDbi_1.8.0 Biobase_2.6.1 > [15] RCurl_1.2-0 bitops_1.0-4.1 RUnit_0.4.22 > > loaded via a namespace (and not attached): > [1] annotate_1.24.1 BSgenome_1.14.2 splines_2.10.1 survival_2.35-8 > tools_2.10.1 XML_2.6-0 xtable_1.5-6 > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 7.6 years ago by Michael Lawrence9.8k
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