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  • GenomicFeatures: makeTranscriptDbFromUCSC suddenly started creating errors

    I've been using the makeTranscriptDbFromUCSC function to retrieve ensembl genes from UCSC for over two years as part of our RNA-Seq expression profiling pipeline. Suddenly, last week, it started generating the following error:

    > txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="ensGene")
    Warning message:
    In .local(.Object, ...) : NAs introduced by coercion
    Error in genome(ucscCart(x)) :
    error in evaluating the argument 'x' in selecting a method for function 'genome': Error in matrix(unlist(pairs), nrow = 2) :
    'data' must be of a vector type

    Has anyone seen this? Any idea why it just started happening and how to fix it?

    > sessionInfo()
    R version 2.15.2 (2012-10-26)
    Platform: x86_64-redhat-linux-gnu (64-bit)

    locale:
    [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
    [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
    [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
    [7] LC_PAPER=C LC_NAME=C
    [9] LC_ADDRESS=C LC_TELEPHONE=C
    [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

    attached base packages:
    [1] stats graphics grDevices utils datasets methods base

    other attached packages:
    [1] GenomicFeatures_1.10.2 AnnotationDbi_1.20.7 Biobase_2.18.0
    [4] GenomicRanges_1.10.7 IRanges_1.16.6 BiocGenerics_0.4.0

    loaded via a namespace (and not attached):
    [1] biomaRt_2.14.0 Biostrings_2.26.3 bitops_1.0-6 BSgenome_1.26.1
    [5] DBI_0.2-7 parallel_2.15.2 RCurl_1.95-4.1 Rsamtools_1.10.2
    [9] RSQLite_0.11.4 rtracklayer_1.18.2 stats4_2.15.2 tools_2.15.2
    [13] XML_3.98-1.1 zlibbioc_1.4.0

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