Hi James,

There have been recent changes to UCSC. Unfortunately, your version of
Bioconductor is too old to be fixed. Please update.

Michael
On May 19, 2014 12:29 PM, "Denvir, James" <denvir@marshall.edu> wrote:

> Hello,
>
> I’ve been using your GenomicFeatures bioconductor package for a few years
> as part of our RNA-Seq data analysis pipeline; specifically, I use it to
> retrieve Ensembl transcripts from UCSC via
>
> txdb <- makeTranscriptDbFromUCSC(genome=“hg19”, tablename=“ensGene”)
>
> (I use this prior to counting overlaps to create count tables for DESeq.)
>
> Suddenly, this has stopped working, and produces the error
>
>
> 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
>
>
>
> Nothing changed in the script between this running successfully, and
> nothing changed in the R setup on my machine (as far as I can tell);
> additionally I tried this on a separate box and got the same error.
>
> I wonder if UCSC changed their URL structures and if this has broken your
> function? My R skills are not really up to diagnosing that.
>
> Any help or suggestions would be much appreciated, though actually my main
> purpose was to alert you to the fact that there may be a general issue.
>
> (I tried a workaround in which I downloaded a GTF from UCSC and used the
> makeTranscriptDbFromGFF function; that has hung  (for about two days) on
> "Deducing exon rank from relative coordinates provided”).
>
> Thanks,
>
> James Denvir, Ph.D.
>
> Assistant Professor of Bioinformatics and Biostatistics
> Department of Biochemistry and Microbiology
>
> Co-Director, Genomics and Bioinformatics Core Facility
>
> Marshall University School of Medicine
> 304-696-7327
>
>
> 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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