Seemed to work for me. Could just be a transient issue with UCSC? On Fri, Oct 16, 2015 at 12:02 PM, Arora, Sonali <[email protected]> wrote: > Hi , > > I get an error when creating a txdb object for hg19 from the refGene Table > >> txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene") > Error in tableNames(ucscTableQuery(session, track = track)) : > error in evaluating the argument 'object' in selecting a method for > function 'tableNames': Error in relist(ans_unlistData, ans_partitioning) : > shape of 'skeleton' is not compatible with 'NROW(flesh)' > > Is this because GenomicRanges() is broken in devel ? Please advise. > > >> sessionInfo() > R Under development (unstable) (2015-10-15 r69519) > Platform: x86_64-w64-mingw32/x64 (64-bit) > Running under: Windows 7 x64 (build 7601) Service Pack 1 > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > States.1252 > > attached base packages: > [1] stats4 parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] GenomicFeatures_1.23.1 AnnotationDbi_1.33.0 Biobase_2.31.0 > GenomicRanges_1.21.32 GenomeInfoDb_1.7.0 > [6] IRanges_2.5.0 S4Vectors_0.9.0 BiocGenerics_0.17.0 > BiocInstaller_1.21.1 > > loaded via a namespace (and not attached): > [1] XVector_0.11.0 zlibbioc_1.17.0 GenomicAlignments_1.7.0 > BiocParallel_1.5.0 > [5] tools_3.3.0 SummarizedExperiment_1.1.0 DBI_0.3.1 > lambda.r_1.1.7 > [9] futile.logger_1.4.1 rtracklayer_1.31.0 futile.options_1.0.0 > bitops_1.0-6 > [13] RCurl_1.95-4.7 biomaRt_2.27.0 RSQLite_1.0.0 > Biostrings_2.39.0 > [17] Rsamtools_1.23.0 XML_3.98-1.3 > > -- > Thanks and Regards, > Sonali > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel
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