R remove stopwords from a character vector using %in%

You are not accessing the list properly and you're not getting the elements back from the result of %in% (which gives a logical vector of TRUE/FALSE). You should do something like this:

unlist(str1)[!(unlist(str1) %in% stopWords)]

(or)

str1[[1]][!(str1[[1]] %in% stopWords)]

For the whole data.frame df1, you could do something like:

'%nin%' <- Negate('%in%')
lapply(df1[,2], function(x) {
    t <- unlist(strsplit(x, " "))
    t[t %nin% stopWords]
})

# [[1]]
# [1] "string"  "string."
# 
# [[2]]
# [1] "string"   "slightly" "string." 
# 
# [[3]]
# [1] "string"  "string."
# 
# [[4]]
# [1] "string"   "slightly" "shorter"  "string." 
# 
# [[5]]
# [1] "string"   "string"   "strings."

First. You should unlist str1 or use lapply if str1 is vector:

!(unlist(str1) %in% words)
#>  [1]  TRUE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE

Second. Complex solution:

string <- c("This string is a string.",
            "This string is a slightly longer string.",
            "This string is an even longer string.",
            "This string is a slightly shorter string.",
            "This string is the longest string of all the other strings.")
rm_words <- function(string, words) {
    stopifnot(is.character(string), is.character(words))
    spltted <- strsplit(string, " ", fixed = TRUE) # fixed = TRUE for speedup
    vapply(spltted, function(x) paste(x[!tolower(x) %in% words], collapse = " "), character(1))
}
rm_words(string, tm::stopwords("en"))
#> [1] "string string."                  "string slightly longer string."  "string even longer string."     
#> [4] "string slightly shorter string." "string longest string strings."