[BioC] Memory limit (vector size) o linux 64bit

[Ivan Porro]

Hi all,

I'm running a script that try to normalise 448 HGU133A Affymetrix arrays, and I
have "The Error" during the ReadAffy():

  Error: cannot allocate vector of size 1770343 Kb

I know about R and OSs adressing limitations, so (according to several posts on
the mailing list) I'm doing that on a  64bit server:

x86_64 GNU/Linux (2x AMD Opteron 275)
R 2.3.1 compiled from source
MemTotal:         7819808 kB
VmallocTotal: 34359738367 kB

that is, 8GB RAM (the difference is probably kept by a on board video) and up to
34TB swap.

I know from R FAQ that  "There are also limits on individual objects. On all
versions of R, the maximum length (number of elements) of a vector is 2^31 - 1
~ 2*10^9"

But: 2.147.483.648  = 2^31  is bigger than 1.770.343.000 bytes (my vector size)

I'm near (above) R physical limitations?

I use batch<-ReadAffy() then I should normalize it with gcrma(), invariantset

thank you in advance,

    Ivan




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