Error: subscript out of bounds when using ucscGenomes() and supportedGenomes() functions in goseq and rtracklayer packages respctively
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mgdrnl • 0
@mgdrnl-14180
Last seen 4.7 years ago

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             
goseq rtracklayer • 1.2k views
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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.

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