[R] processing a large matrix

[andy1983]

I would like to compare every column in my matrix with every other column and
get the r-squared.

I tried using the following formula and looping through every column:
> summary(lm(matrix[,x]~matrix[,y]))$r.squared
If I have 10,000 columns, the loops (10,000 * 10,000) take forever even if
there is no formula inside.

Then, I attempted to vectorize my code:
> cor(matrix)^2
With 10,000 columns, this works great. With 30,000, R tells me it cannot
allocate vector of that length even if the memory limit is set to 4 GBs.

Is there anything else I can do to resolve this issue?

Thanks.
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