[R] vector memory allocation?
Sam Yeaman
yeaman at zoology.ubc.ca
Sat Mar 5 01:08:59 CET 2005
Hi all,
I have a vector size allocation problem with R 2.0.1 (script and output
shown):
> var1 <- sum (input1 * input2, na = TRUE)
> gc()
used (Mb) gc trigger (Mb)
Ncells 199327 5.4 785113 21.0
Vcells 71039552 542.0 206003790 1571.7
> var2 <- sum (input1 * input2 / input2, na = TRUE)
Error: cannot allocate vector of size 524288 Kb
input1 and input2 are matrices input from text files of about 100 MB.
This error happens irrespective of whether I calculate var1 or var2
first...it will always calculate the first and always have an error on
the second. Am I misusing the garbage-collector? I am confused by the
fact that the difference between 'trigger' and 'used' seems so much
higher than the size of vector that it says it can't allocate.
thanks, Sam Yeaman
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