I'm trying to set up the software for the rapid design of PLAYR probes, as described in this paper: https://www.nature.com/articles/nmeth.3742#supplementary-information
I'm using the GenomicFeatures library, but this line is giving me an error message. Here's the line, followed by the error message, followed by the output of traceback().
> txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene") Error in tableNames(ucscTableQuery(session, track = track)) : error in evaluating the argument 'object' in selecting a method for function 'tableNames': Error in normArgTrack(track, trackids) : Unknown track: RefSeq Genes > traceback() 2: tableNames(ucscTableQuery(session, track = track)) 1: makeTxDbFromUCSC(genome = "hg19", tablename = "refGene")
I've read the documentation of the makeTxDbFromUCSC function available here: https://bioconductor.org/packages/release/bioc/manuals/GenomicFeatures/man/GenomicFeatures.pdf, but I'm having a hard time understanding the error message.
As suggested by the Posting Guide, here's the output of sessionInfo(). Let me know if I need to provide any other information.
> sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS 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=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicFeatures_1.22.13 AnnotationDbi_1.32.3 Biobase_2.30.0 [4] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 IRanges_2.4.8 [7] S4Vectors_0.8.11 BiocGenerics_0.16.1 PLAYRDesign_0.1 [10] RSQLite_2.1.0 devtools_1.13.5 BiocInstaller_1.20.3 loaded via a namespace (and not attached): [1] Rcpp_0.12.16 plyr_1.8.4 [3] git2r_0.21.0 futile.logger_1.4.3 [5] XVector_0.10.0 AnnotationFuncs_1.20.0 [7] bitops_1.0-6 futile.options_1.0.0 [9] tools_3.2.3 zlibbioc_1.16.0 [11] biomaRt_2.26.1 digest_0.6.15 [13] bit_1.1-12 lattice_0.20-35 [15] memoise_1.1.0 BSgenome_1.38.0 [17] pkgconfig_2.0.1 shiny_1.0.5 [19] DBI_0.8 curl_3.2 [21] stringr_1.3.0 rtracklayer_1.30.4 [23] withr_2.1.2 httr_1.3.1 [25] Biostrings_2.38.4 grid_3.2.3 [27] bit64_0.9-7 R6_2.2.2 [29] BSgenome.Hsapiens.UCSC.hg19_1.4.0 tcltk_3.2.3 [31] XML_3.98-1.11 BiocParallel_1.4.3 [33] magrittr_1.5 reshape2_1.4.3 [35] org.Hs.eg.db_3.2.3 lambda.r_1.2 [37] blob_1.1.1 htmltools_0.3.6 [39] Rsamtools_1.22.0 GenomicAlignments_1.6.3 [41] SummarizedExperiment_1.0.2 xtable_1.8-2 [43] mime_0.5 httpuv_1.3.6.2 [45] stringi_1.1.7 RCurl_1.95-4.10 [47] zoo_1.8-1
Your version of R, Bioconductor, and GenomicFeatures appears to be out-of-date. Updgrading your version of R to the current release and following the instructions to update Bioconductor may solve the issue.