subset() fails with zero-dimension objects and missing values

[mtmorgan]

Compare

> subset(DataFrame())
Error: subscript is a logical vector with out-of-bounds TRUE values
> subset(data.frame())
data frame with 0 columns and 0 rows

This is because

S4Vectors/R/eval-utils.R

Line 47 in b14a989

TRUE

returns a length 1 logical vector regardless the dimensions of x.

This is the reason for Bioconductor/VariantAnnotation#40, with j incorrect at https://github.com/Bioconductor/VariantAnnotation/blob/61ecbd8e019cd3e15013506fc5ec6a4495829f7c/R/methods-VCF-class.R#L336

[hpages]

@lawremi Michael?