# [R] Memory problems...leaky?

Sam Yeaman yeaman at zoology.ubc.ca
Thu Nov 18 23:38:02 CET 2004

```Hi list folks,

I have been trying to figure out how I can run the script that I have
included below. I have 1.2 gigs of memory on the computer, but this is
not enough, given the size of the input datasets. The input matrix
('input') is a little under 2400 x 2900 cells, and is about 60 megs when
stored on hard drive...what is R doing, that this (small) size of file
takes up so much memory? The script uses three variables of this size,
but  I don't see why that would add up to over 1.2 gigs...Is the way
that I call variables in the for-loops causing this problem, with some
sort of leakiness? I had heard of leaky memory problems with version
1.5.1, but I am using 1.9.1. Alternatively, I had wondered if it was
just the way memory works in R, as I had read a post earlier today that
suggested that R requires 5-10 times more memory than the input to
meaninfully calculate anything...

Thanks...Sam

bflow <- 2
pie <- 3.141592654

rowsize <- dim(input)[1]
colsize <- dim(input)[2]

result <- matrix (NA, rowsize, colsize)

for (i in 1:rowsize)
for (j in 1:colsize)

if (is.na (input [i,j]) == FALSE) {

probability <- matrix (NA, rowsize, colsize)

for (p in 1:rowsize) {
or (q in 1:colsize){
distance <- sqrt ((p - i)^2 + (q - j)^2)
probability [p,q] <- (2 / (bflow * pie * (1 + (distance /
bflow)^2)))
}
}

kernsum <- sum ((probability * input / input), na =
TRUE)
intmean <- sum (input * probability, na = TRUE) /
kernsum
result [i,j] <- sum (((input - intmean)^2 * probability), na =
TRUE) / kernsum
}

}
}

```