well that's odd. managed to get the same error using the most kosher
workflow I could find:
> vcfFile <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
> from <- vcfFile
> to <- tempfile()
> compressVcf <- bgzip(from, to)
> idx <- indexTabix(compressVcf, "vcf")
> tab <- TabixFile(compressVcf, idx)
> rng <- GRanges(seqnames="20", ranges=IRanges(start=c(250000,
500000),end=c(300000,600000)))
> myparam<-ScanVcfParam(which=rng)
> vcf <- readVcf(tab, "hg19",myparam)
Error in lapply(names(vcf[[1]]), function(elt) { :
  error in evaluating the argument 'X' in selecting a method for function
'lapply': Error in vcf[[1]] : subscript out of bounds
> sessionInfo()
R version 3.0.1 (2013-05-16)
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] parallel  stats     graphics  utils     datasets  grDevices methods
[8] base

other attached packages:
[1] VariantAnnotation_1.6.7 Rsamtools_1.12.4        Biostrings_2.28.0
[4] GenomicRanges_1.12.5    IRanges_1.18.4          BiocGenerics_0.6.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.22.6   Biobase_2.20.1         biomaRt_2.16.0
 [4] bitops_1.0-6           BSgenome_1.28.0        DBI_0.2-7
 [7] GenomicFeatures_1.12.4 RCurl_1.95-4.1         RSQLite_0.11.4
[10] rtracklayer_1.20.4     stats4_3.0.1           tools_3.0.1
[13] XML_3.98-1.1           zlibbioc_1.6.0

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