[R] progressive slowdown during script execution?

[Tim Alcon]

I'm an R novice, so I hope my question is a valid one.  I'm trying to 
run the following script in the current version of R.

for (i in 1:1640){for (j in (i+1):1641){
if (i == 1 && j == 2){x <- cor(sage[i,],sage[j,],method="spearman"); y 
<- cor(frie[i,],frie[j,],method="spearman")}
if (i != 1 || j != 2){x <- 
c(x,cor(sage[i,],sage[j,],method="spearman")); y <- 
c(y,cor(frie[i,],frie[j,],method="spearman"))}}}

It basically just finds all pairwise correlations of the rows in a 
matrix for each of two matrices and stores the results for each matrix 
in a vector.  The problem I seem to be running into is that it seems to 
slow way down during execution somehow.  When I first tried running it I 
stopped execution to see how fast it was running, before trying to 
compute the whole job (the two matrices each have 1641 rows).  Based on 
what I saw, I figured it would easily finish overnight.  Instead, it was 
still running almost 24 hours later.  To quantify this a little better I 
checked it after running for 5 minutes, at which point it had added 
79120 correlations to each of the x and y vectors.  Since there should 
be a total of (1641*1640)/2 = 1345620 pairwise correlations in each 
vector when it finishes running, I worked out that it should take 
(1345620/79120)*5 = 85 minutes to run the whole job.  However, when I 
checked it after running for 2 hours, it had added only 341870 
correlations to each vector.

Any ideas what I'm doing wrong, or why it would run more slowly the 
longer it runs?  Thanks for any help or advice.

Tim