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Hello
I got this error when using supportedGenomes() in goseq package:
> library(goseq) Loading required package: BiasedUrn Loading required package: geneLenDataBase > head(supportedGenomes()) Error in getNodeSet(doc, "//table[@class='descTbl']")[[1L]] : subscript out bounds
I got the same error when using ucscGenomes() function from rtracklayer package. supportedGenomes() function uses ucscGenomes(), so I guess the source of the error is in this function. Any help will be helpful!
> sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.4 LTS locale: [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C LC_TIME=es_ES.UTF-8 [4] LC_COLLATE=es_ES.UTF-8 LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8 [7] LC_PAPER=es_ES.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.32.2 GenomicRanges_1.24.3 GenomeInfoDb_1.8.7 IRanges_2.6.1 [5] S4Vectors_0.10.1 BiocGenerics_0.18.0 goseq_1.24.0 geneLenDataBase_1.8.0 [9] BiasedUrn_1.07 loaded via a namespace (and not attached): [1] AnnotationDbi_1.34.3 XVector_0.12.1 zlibbioc_1.18.0 [4] GenomicAlignments_1.8.4 BiocParallel_1.6.6 lattice_0.20-33 [7] tools_3.3.1 grid_3.3.1 SummarizedExperiment_1.2.3 [10] nlme_3.1-128 Biobase_2.32.0 mgcv_1.8-12 [13] DBI_0.4-1 Matrix_1.2-6 bitops_1.0-6 [16] RCurl_1.95-4.8 biomaRt_2.28.0 RSQLite_1.0.0 [19] GO.db_3.3.0 GenomicFeatures_1.24.5 Biostrings_2.40.2 [22] Rsamtools_1.24.0 XML_3.98-1.1
Unable to reproduce this. Maybe it was just a transient issue, or something to do with your network. Either way, we no longer support your version of Bioconductor.