[Bioc-devel] Error in GenomicFeatures::makeTxDbFromUCSC()
Hi Sonali, Michael, Tried on Linux and Windows with BioC 3.3 and couldn't reproduce this either (got the expected/usual warning about the cds cumulative length not being a multiple of 3). BTW I think GenomicRanges is failing in the devel builds because of some issues with AnnotationHub. I don't think this is related to the error you got with makeTxDbFromUCSC() though. H.
On 10/16/2015 12:55 PM, Michael Lawrence wrote:
Seemed to work for me. Could just be a transient issue with UCSC? On Fri, Oct 16, 2015 at 12:02 PM, Arora, Sonali <sarora at fredhutch.org> 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
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