`grepl` isn't working correctly for `CharacterList` with `ignore.case` and `fixed` enabled

[mjsteinbaugh]

Hi Bioconductor team,

I noticed an issue with grepl matching against a CharacterList object:

library(IRanges)
pattern <- "a"
x <- CharacterList(list(c("A", "a"), c("B", "b")))
print(x)
## CharacterList of length 2
## [[1]] A a
## [[2]] B b

This works as expected:

grepl(pattern = pattern, x = x, ignore.case = FALSE, fixed = FALSE)
## LogicalList of length 2
## [[1]] FALSE TRUE
## [[2]] FALSE FALSE

This works as expected:

grepl(pattern = pattern, x = x, ignore.case = FALSE, fixed = TRUE)
## LogicalList of length 2
## [[1]] FALSE TRUE
## [[2]] FALSE FALSE

This works as expected:

grepl(pattern = pattern, x = x, ignore.case = TRUE, fixed = FALSE)
## LogicalList of length 2
## [[1]] TRUE TRUE
## [[2]] FALSE FALSE

This doesn't work as expected. Warns and returns incorrect values. Should return [[1]] TRUE TRUE.

grepl(pattern = pattern, x = x, ignore.case = TRUE, fixed = TRUE)
## Warning in grepl(pattern, unlist(x, use.names = FALSE), ignore.case, perl,  :
##   argument 'ignore.case = TRUE' will be ignored
## Calls: grepl -> grepl -> relist -> grepl -> grepl
## LogicalList of length 2
## [[1]] FALSE TRUE
## [[2]] FALSE FALSE

Best,
Mike

[hpages]

Should return [[1]] TRUE TRUE.

Are you sure?

base::grepl(pattern = "a", x = c("A", "a"), ignore.case = TRUE, fixed = TRUE)
# [1] FALSE  TRUE
# Warning message:
# In base::grepl(pattern = "a", x = c("A", "a"), ignore.case = TRUE,  :
#   argument 'ignore.case = TRUE' will be ignored

[mjsteinbaugh]

@hpages argument 'ignore.case = TRUE' will be ignored shouldn't be happening though right? This is confusing behavior in R.

grepl(pattern = "a", x = c("A", "a"), ignore.case = TRUE, fixed = FALSE)
## [1] TRUE TRUE

grepl(pattern = "a", x = c("A", "a"), ignore.case = TRUE, fixed = TRUE)
## Warning in grepl(pattern = "a", x = c("A", "a"), ignore.case = TRUE, fixed = TRUE) :
##   argument 'ignore.case = TRUE' will be ignored
## [1] FALSE  TRUE

Ah you're right thanks -- I'm going to close and make sure I don't use fixed. This seems like a bug in base R to me.