[Rd] Severe memory problem using split()

cstrato cstrato at aon.at
Mon Jul 12 22:45:43 CEST 2010

Dear all,

With great interest I followed the discussion:
since I have currently a similar problem:

In a new R session (using xterm) I am importing a simple table 
"Hu6800_ann.txt" which has a size of 754KB only:

 > ann <- read.delim("Hu6800_ann.txt")
 > dim(ann)
[1] 7129   11

When I call "object.size(ann)" the estimated memory used to store "ann" 
is already 2MB:

 > object.size(ann)
2034784 bytes

Now I call "split()" and check the estimated memory used which turns out 
to be 3.3GB:

 > u2p  <- split(ann[,"ProbesetID"],ann[,"UNIT_ID"])
 > object.size(u2p)
3323768120 bytes

During the R session I am running "top" in another xterm and can see 
that the memory usage of R increases to about 550MB RSIZE.

Now I do:

 > object.size(unlist(u2p))
894056 bytes

It takes about 3 minutes to complete this call and the memory usage of R 
increases to about 1.3GB RSIZE. Furthermore, during evaluation of this 
function the free RAM of my Mac decreases to less than 8MB free PhysMem, 
until it needs to swap memory. When finished, free PhysMem is 734MB but 
the size of R increased to 577MB RSIZE.

Doing "split(ann[,"ProbesetID"],ann[,"UNIT_ID"],drop=TRUE)" did not 
change the object.size, only processing was faster and it did use less 
memory on my Mac.

Do you have any idea what the reason for this behavior is?
Why is the size of list "u2p" so large?
Do I make any mistake?

Here is my sessionInfo on a MacBook Pro with 2GB RAM:

 > sessionInfo()
R version 2.11.1 (2010-05-31)

[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

Best regards
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at

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