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Since updating to R-3.3.3 yesterday (not clear if related) I get the following error when using BiomartGeneRegionTrack:
library(Gviz) BiomartGeneRegionTrack(symbol = "Stat1", genome = "mm9") Error in .Primitive("c")() : could not find symbol "recursive" in environment of the generic function
EDIT: Just tested this with release_base2 docker image (that uses R-3.3.2) and installing Gviz package and it runs without problem.
Further information:
> traceback() 12: .Primitive("c")() 11: do.call(c, args) 10: do.call(c, args) 9: .local(x, ..., na.rm = na.rm) 8: range(, na.rm = FALSE) 7: range(, na.rm = FALSE) 6: .cacheMartData(.Object, chromosome, staged) 5: .local(.Object, ...) 4: initialize(value, ...) 3: initialize(value, ...) 2: new("BiomartGeneRegionTrack", start = start, end = end, chromosome = chromosome, strand = strand, biomart = biomart, name = name, genome = genome, stacking = stacking, filter = filters, featureMap = featureMap, symbol = symbol, gene = gene, transcript = transcript, entrez = entrez, ...) 1: BiomartGeneRegionTrack(symbol = "Stat1", genome = "mm9") > sessionInfo() R version 3.3.3 (2017-03-06) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra 10.12.3 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid parallel stats4 stats graphics grDevices utils [8] datasets methods base other attached packages: [1] Gviz_1.18.1 GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 [4] IRanges_2.8.1 S4Vectors_0.12.1 BiocGenerics_0.20.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.9 biovizBase_1.22.0 [3] lattice_0.20-34 Rsamtools_1.26.1 [5] Biostrings_2.42.1 assertthat_0.1 [7] digest_0.6.12 mime_0.5 [9] R6_2.2.0 plyr_1.8.4 [11] backports_1.0.5 acepack_1.4.1 [13] RSQLite_1.1-2 BiocInstaller_1.24.0 [15] httr_1.2.1 ggplot2_2.2.1 [17] zlibbioc_1.20.0 GenomicFeatures_1.26.3 [19] lazyeval_0.2.0 data.table_1.10.4 [21] rpart_4.1-10 Matrix_1.2-8 [23] checkmate_1.8.2 splines_3.3.3 [25] BiocParallel_1.8.1 AnnotationHub_2.6.4 [27] stringr_1.2.0 foreign_0.8-67 [29] htmlwidgets_0.8 RCurl_1.95-4.8 [31] biomaRt_2.30.0 munsell_0.4.3 [33] shiny_1.0.0 httpuv_1.3.3 [35] rtracklayer_1.34.2 base64enc_0.1-3 [37] htmltools_0.3.5 nnet_7.3-12 [39] SummarizedExperiment_1.4.0 tibble_1.2 [41] gridExtra_2.2.1 htmlTable_1.9 [43] interactiveDisplayBase_1.12.0 Hmisc_4.0-2 [45] matrixStats_0.51.0 XML_3.98-1.5 [47] GenomicAlignments_1.10.0 bitops_1.0-6 [49] xtable_1.8-2 gtable_0.2.0 [51] DBI_0.5-1 magrittr_1.5 [53] scales_0.4.1 stringi_1.1.2 [55] XVector_0.14.0 latticeExtra_0.6-28 [57] Formula_1.2-1 RColorBrewer_1.1-2 [59] ensembldb_1.6.2 tools_3.3.3 [61] dichromat_2.0-0 BSgenome_1.42.0 [63] Biobase_2.34.0 yaml_2.1.14 [65] survival_2.40-1 AnnotationDbi_1.36.2 [67] colorspace_1.3-2 cluster_2.0.5 [69] memoise_1.0.0 VariantAnnotation_1.20.2 [71] knitr_1.15.1
This is fixed following A: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC) (setting t
ype = "source"
and installing GenomicRanges).