Entering edit mode
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,
>
> Iâve 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=âhg19â,
tablename=âensGeneâ)
>
> (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 providedâ).
>
> 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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