Matching a sequence in a larger vector

Try rollapply in zoo:

library(zoo)
which(rollapply(y, 2, identical, c("a", "a")))
## [1] 1 2
which(rollapply(y, 2, identical, c("a", "b")))
## [1] 3

set.seed(0)
a <- sample(1:6,12000, TRUE)
b <- 2:4

vecIn <- function(a,b){
which(
Reduce('+', lapply(seq_along(y <- lapply(b, '==', a)), function(x){
                                            y[[x]][x:(length(a) - length(b) +x)]
                                           }
                  )
      ) == length(b)
     )
} 

> vecIn(a,b)
 [1]     2   154   986  1037  1046  1257  1266  1750  2375  2677  3184  3206
[13]  3499  3526  3882  4238  4311  4388  4437  4580  4714  4766  4827  5046
[25]  5279  5629  6153  6842  6856  6919  7200  7516  7520  7707  7824  7859
[37]  8140  8191  8687  9208  9281  9313 10022 10320 10617 10720 10958 11179
[49] 11567 11591 11698 11811

library(zoo)
library(rbenchmark)

func1 <- function(a,b){
 gregexpr(paste0(b,collapse=""),paste0(a,collapse=""))
}

func2 <- function(a,b){
 which(rollapply(a, length(b), identical, b))
}

func3 <- vecIn

Some benchmarks

benchmark(func1(a,b), func2(a,b), func3(a,b))
         test replications elapsed relative user.self sys.self user.child
1 func1(a, b)          100   0.673    5.904     0.680    0.000          0
2 func2(a, b)          100  28.808  252.702    28.198    0.672          0
3 func3(a, b)          100   0.114    1.000     0.116    0.000          0
  sys.child
1         0
2         0
3         0