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 > [[alternative HTML version deleted]]