[Bioc-devel] Error in GenomicFeatures::makeTxDbFromUCSC()

[Michael Lawrence]

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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