I met some issue by running examples in R package VariantAnnotation:
> library(VariantAnnotation)
> fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
> fl
[1] "/usr/local/lib/R/site-library/VariantAnnotation/extdata/ex2.vcf"
> scanVcfHeader(fl)
Error in c(DataFrameList(META = meta), tbls[unique(tags)]) :
could not find symbol "recursive" in environment of the generic function
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] VariantAnnotation_1.20.2 Rsamtools_1.26.1 Biostrings_2.42.1 XVector_0.14.0 SummarizedExperiment_1.4.0 Biobase_2.34.0
[7] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 IRanges_2.8.1 S4Vectors_0.12.1 BiocGenerics_0.20.0 setwidth_1.0-4
[13] colorout_1.1-2
loaded via a namespace (and not attached):
[1] Rcpp_0.12.9 AnnotationDbi_1.36.2 GenomicAlignments_1.10.0 zlibbioc_1.20.0 BiocParallel_1.8.1 BSgenome_1.42.0 lattice_0.20-34
[8] tools_3.3.3 grid_3.3.3 DBI_0.6 digest_0.6.12 Matrix_1.2-8 rtracklayer_1.34.2 bitops_1.0-6
[15] biomaRt_2.30.0 RCurl_1.95-4.8 memoise_1.0.0 RSQLite_1.1-2 GenomicFeatures_1.26.3 XML_3.98-1.5
Hi,
I still have this problem with the new version of VariantAnnotation (1.20.3).
If it's not solved yet, Martin Morgan 's solution A: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC) worked well for me. :D