[Bioc-devel] Strange "internal logical NA value has been modified" error

Hi Herv?,

On 10/13/21 12:43 PM, Herv? Pag?s wrote:

On 12/10/2021 15:43, Pariksheet Nanda wrote:

The function in question is:

replace_unstranded <- function (gr) {
???? idx <- strand(gr) == "*"
???? if (length(idx) == 0L)

??????????? ^^^^^^^^^^^^^^^^^
Not related to the "internal logical NA value has been modified" error
but shouldn't you be doing '!any(idx)' instead of 'length(idx) == 0L' 
here?

Indeed.? Although in a roundabout way the result somehow satisfied the 
unit tests, idx is a poor choice of name because it's really a mask, and 
your suggestion of OR-ing the mask FALSE values with any() is more 
intuitive.? The name is_unstranded might be less cryptic than mask.

Applying your suggestion of the correct condition uncovered a bug where 
return(gr) was returning the unsorted value, which is inconsistent with 
the behavior of the final statement returns a sorted value.? So changed 
to return(sort(gr)) for a consistent contract.

Fixed in f6892ea

Best,
H.

???????? return(gr)
???? sort(c(
???????? gr[! idx],
???????? `strand<-`(gr[idx], value = "+"),
???????? `strand<-`(gr[idx], value = "-")))
}

Pariksheet