storing long strings (DNA sequence) in R

Question

I have written a function that finds the indices of subsequences in a long DNA sequence. It works when my longer DNA sequence is < about 4000 characters. However, when I try to apply the same function to a much longer sequence, the console gives me a + instead of a >... which leads me to believe that it is the length of the string that is the problem.

for example: when the longer sequence is: "GATATATGCATATACTT", and the subsequence is: "ATAT", I get the indices "1, 3, 9" (0-based)

dnaMatch <- function(dna, sequence) {
  ret <- list()
  k <- str_length(sequence)
  c <- str_length(dna) - k 
  for(i in 1:(c+1)) {
    ret[i] = str_sub(dna, i, i+k-1)
  }
  ret <- unlist(ret)
  TFret <- lapply (ret, identical, sequence)
  TFret <- which(unlist(TFret), arr.ind = TRUE) -1
  print(TFret)
}

Basically, my question is... is there any way around the character-limitation in the string class?

Answer 1

I can replicate nrussell's example, but this assigns correctly x<-paste0(rep("abcdef",1000),collapse="") -- a potential workaround is writing the character string to a .txt file and reading the .txt file into R directly:

test.txt is a 6,000 character long string.

`test<-read.table('test.txt',stringsAsFactors = FALSE)
 length(class(test[1,1]))
[1] 1
class(test[1,1])
[1] "character"
 nchar(test[1,1])
[1] 6000`