The code used for benchmarking

Benchmark SO

library(stringr)
library(microbenchmark)
str<-c("3412123401234")

replength<-function(pat,s) {
  length( gregexpr(pat,s)[[1]] )
}

repeats<-function(s) {
  r<-sapply(
    unique(
      regmatches( s, gregexpr("(\\d{2,})(?=.*\\1)", s, perl=T) )[[1]]
    ),
    replength,s=s )
  pat<-names(r[r==max(r)][1])
  data.frame("Pattern"=pat,"Repeats"=unname(r[r==max(r)][1]),"Pat.length"=nchar(pat),stringsAsFactors=FALSE)
}

tensibai<-function(str) {
  repeats(str)
}

make.matrix <- function(x,y) {
  vl <- nchar(d)
  OUT <- seq(x,nchar(y),1)
  if(length(OUT) < vl) OUT <- c(OUT,rep(NA,vl-length(OUT)))
  OUT
}
 
jimbou <- function(d) {
  mm <- sapply(1:nchar(d), make.matrix, d)  
  mm2 <- sapply(2:nrow(mm), function(x,y) str_sub(string= y, start= mm[1,], end= mm[x,]), d)
  counts <- sort(table(mm2),decreasing = T)
  res <- data.frame("nlength"=sapply(names(counts),nchar),"counts"=counts)
  res[res$counts>1,]
}

original <- function(string){
  out = c()
  check.till = floor(nchar(string)/2)
  for (start in 1:nchar(string)){
    for (end in 1:check.till){
      pat = substr(string,start,start+end)
      repeats = length(gregexpr(pat,string)[[1]])
      length = nchar(pat)
      if (length >= 2) out = rbind(out, c(pat, repeats, length))
    }
  }
  out = as.data.frame(out, stringsAsFactors = FALSE)
  colnames(out) = c("Pattern","Repeats","Pat.Length")
  out$Repeats = as.integer(out$Repeats)
  out$Pat.Length = as.integer(out$Pat.Length)
  out = out[out$Repeats > 1,]
  out = out[order(out[,2],out[,3],decreasing = T),]
  out = out[1,]
  out[is.na(out)] = 0
  return(out)
}

microbenchmark(original(str),jimbou(str),tensibai(str),times=3)