Restart your computer. (Yeah, I know that what the help-desk always
says.)
Start R before doing anything else.
Then run your code in a clean session. Check ls() oafter starte up to
make sure you don't have a bunch f useless stuff in your .Rdata
file. Don't load anything that is not germane to this problem. Use
this function to see what sort of space issues you might have after
loading objects:
getsizes <- function() {z <- sapply(ls(envir=globalenv()),
function(x) object.size(get(x)))
(tmp <- as.matrix(rev(sort(z))[1:10]))}
Then run your code.
--
David.
On Nov 2, 2010, at 10:13 PM, Lorenzo Cattarino wrote:
I would also like to include details on my R version
version _
platform x86_64-pc-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
from FAQ 2.9
(http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-b
e-a-limit-on-the-memory-it-uses_0021
<http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-b
e-a-limit-on-the-memory-it-uses_0021> ) it says that:
"For a 64-bit build, the default is the amount of RAM"
So in my case the amount of RAM would be 4 GB. R should be able to
allocate a vector of size 5 Mb without me typing any command (either
as
memory.limit() or appended string in the target path), is that right?
From: Lorenzo Cattarino
Sent: Wednesday, 3 November 2010 10:55 AM
To: 'r-help@r-project.org'
Subject: memory allocation problem
I forgot to mention that I am using windows 7 (64-bit) and the R
version
2.11.1 (64-bit)
From: Lorenzo Cattarino
I am trying to run a non linear parameter optimization using the
function optim() and I have problems regarding memory allocation.
My data are in a dataframe with 9 columns. There are 656100 rows.
head(org_results)
comb.id p H1 H2 Range Rep no.steps dist aver.hab.amount
1 1 0.1 0 0 1 100 0
0.2528321 0.1393901
2 1 0.1 0 0 1 100 0
0.4605934 0.1011841
3 1 0.1 0 0 1 100 4
3.4273670 0.1052789
4 1 0.1 0 0 1 100 4
2.8766364 0.1022138
5 1 0.1 0 0 1 100 0
0.3496872 0.1041056
6 1 0.1 0 0 1 100 0
0.1050840 0.3572036
est_coeff <- optim(coeff,SS, steps=org_results$no.steps,
Range=org_results$Range, H1=org_results$H1, H2=org_results$H2,
p=org_results$p)
Error: cannot allocate vector of size 5.0 Mb
In addition: Warning messages:
1: In optim(coeff, SS, steps = org_results$no.steps, Range =
org_results$Range, : Reached total allocation of 10000Mb: see
help(memory.size)
2: In optim(coeff, SS, steps = org_results$no.steps, Range =
org_results$Range, : Reached total allocation of 10000Mb: see
help(memory.size)
3: In optim(coeff, SS, steps = org_results$no.steps, Range =
org_results$Range, : Reached total allocation of 10000Mb: see
help(memory.size)
4: In optim(coeff, SS, steps = org_results$no.steps, Range =
org_results$Range, : Reached total allocation of 10000Mb: see
help(memory.size)
memory.size()
[1] 9978.19
memory.limit()
[1] 10000
I know that I am not sending reproducible codes but I was hoping that
you could help me understand what is going on. I set a maximum limit
of
10000 mega byte (by writing this string --max-mem-size=10000M after
the
target path, right click on R icon, shortcut tab). And R is telling me
that it cannot allocate a vector of size 5 Mb???
David Winsemius, MD
West Hartford, CT
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