Question: Error of Memory Size in R
1
gravatar for 12021560-040
2.9 years ago by
12021560-04060
Pakistan
12021560-04060 wrote:
> rawData <- read.celfiles(celfiles)
Platform design info loaded.
Reading in : GSE42902/CEL/GSM1053073_S0608F0055a.CEL.gz
Reading in : GSE42902/CEL/GSM1053074_S0608F0051.CEL.gz
Reading in : GSE42902/CEL/GSM1053075_S0608F0048.CEL.gz
Reading in : GSE42902/CEL/GSM1053076_S0608F0046.CEL.gz
Reading in : GSE42902/CEL/GSM1053077_S0608F0057.CEL.gz
Reading in : GSE42902/CEL/GSM1053078_S0608F0049.CEL.gz
Reading in : GSE42902/CEL/GSM1053079_S0608F0045.CEL.gz
Reading in : GSE42902/CEL/GSM1053080_S0608F0047.CEL.gz
Reading in : GSE42902/CEL/GSM1053081_S0608F0059.CEL.gz
Reading in : GSE42902/CEL/GSM1053082_S0608F0052.CEL.gz
Reading in : GSE42902/CEL/GSM1053083_S0608F0060.CEL.gz
Reading in : GSE42902/CEL/GSM1053084_S0608F0056.CEL.gz
Reading in : GSE42902/CEL/GSM1053085_S0608F0058.CEL.gz
Reading in : GSE42902/CEL/GSM1053086_S0608F0050.CEL.gz
Reading in : GSE42902/CEL/GSM1053087_S0608F0054.CEL.gz
Reading in : GSE42902/CEL/GSM1053088_S0608F0053.CEL.gz
Error: cannot allocate vector of size 800.0 Mb
In addition: Warning messages:
1: In dimnames(elt) <- lapply(dimnames(elt), unname) :
  Reached total allocation of 1941Mb: see help(memory.size)
2: In dimnames(elt) <- lapply(dimnames(elt), unname) :
  Reached total allocation of 1941Mb: see help(memory.size)
3: In dimnames(elt) <- lapply(dimnames(elt), unname) :
  Reached total allocation of 1941Mb: see help(memory.size)
4: In dimnames(elt) <- lapply(dimnames(elt), unname) :
  Reached total allocation of 1941Mb: see help(memory.size)
> rawData
character(0)

I have Run this command but error occured and also Character count is (0). Please can anyone Help me to sort this error.

limma affy oligo bioconductor • 1.6k views
ADD COMMENTlink modified 2.9 years ago by Shamim Sarhadi210 • written 2.9 years ago by 12021560-04060

How much memory do you have on this machine? Are you using 32-bit R and/or OS? Are you able to load a smaller number of files (~5)?

ADD REPLYlink written 2.9 years ago by genomax65k
1
gravatar for Antonio R. Franco
2.9 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

It seems that you need a computer with more RAM resources Hoping you are not using a 32bits R, since it can allocate less memory than a 64 bits R

ADD COMMENTlink written 2.9 years ago by Antonio R. Franco4.0k

I have used 64bit R and also my window is 64bits.. But still facing this problem. :(

ADD REPLYlink written 2.9 years ago by 12021560-04060

Still is needed to be known the amount of RAM memory set in your computer. What operative system are you using ?

In addition, run this commands into R

memory.limit() # It will provide the memory available

And read this article

ADD REPLYlink written 2.9 years ago by Antonio R. Franco4.0k
0
gravatar for Shamim Sarhadi
2.9 years ago by
IRAN
Shamim Sarhadi210 wrote:

Suppose you need 2000 memory size, I think you could simply run this code memory.limit(size=2000) and then run your script(also you could give more size to your memory size), In my case I set my machine memory size to 190000

ADD COMMENTlink written 2.9 years ago by Shamim Sarhadi210
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