Hi Michael, Updating XML (and rJava, since I was at it) removed the problem nicely. Thank you. rtracklayer is a very impressive piece of software. Nice work. - Paul On Jan 26, 2009, at 7:26 AM, Michael Lawrence wrote: > > > On Mon, Jan 26, 2009 at 5:06 AM, Paul Shannon <pshannon at="" systemsbiology.org=""> > wrote: > I am following the vignette provided by the 1.2.2 rtracklayer > package -- and delighted to find such capabilities in bioc! > > When I call, browseGenome(subTargetTrack) > > I get this error (with traceback and sessionInfo to follow). Can > anyone help? > > Not sure what happened here, as it's specified in DESCRIPTION, but > somehow your XML version (1.95) does not match the requirements of > rtracklayer (1.98). Please upgrade your XML package and see if that > works. > > Thanks, > Michael > > > - Paul > > Error in as.numeric(hgsid) : > cannot coerce type 'externalptr' to vector of type 'double' > > traceback () > 5: browserView(<s4 object="" of="" class="" "ucscsession"="">, <s4 object="" of=""> class "genomeSegment">) > 4: browserView(<s4 object="" of="" class="" "ucscsession"="">, <s4 object="" of=""> class "genomeSegment">) > 3: do.call("browserView", viewParams) > 2: browseGenome(subTargetTrack) > 1: browseGenome(subTargetTrack) > > sessionInfo () > R version 2.8.1 (2008-12-22) > i386-apple-darwin8.11.1 > > locale: > en_US.US-ASCII/en_US.US-ASCII/C/C/en_US.US-ASCII/en_US.US-ASCII > > attached base packages: > [1] splines tools stats graphics grDevices utils > datasets methods base > > other attached packages: > [1] rtracklayer_1.2.2 RCurl_0.94-0 org.Hs.eg.db_2.2.6 > microRNA_1.0.0 Rlibstree_0.3-1 matchprobes_1.14.1 > affy_1.20.2 > [8] limma_2.16.4 genefilter_1.22.0 survival_2.34-1 > humanStemCell_0.2.0 hgu133plus2.db_2.2.5 RSQLite_0.6-9 > DBI_0.2-4 > [15] AnnotationDbi_1.4.2 Biobase_2.2.1 > > loaded via a namespace (and not attached): > [1] Biostrings_2.10.15 IRanges_1.0.9 Matrix_0.999375-18 > XML_1.95-2 affyio_1.8.0 annotate_1.20.1 > grid_2.8.1 > [8] lattice_0.17-17 preprocessCore_1.4.0 rJava_0.5-1 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >