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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).