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hi everyone,
I tried to run my code in RStudio,but I received this error message,what should
I do?
Error: cannot allocate vector of size 12.1 Gb
In addition: Warning messages:
1: In cor(coding.rpkm[grep("23.C", coding.rpkm$name), -1],
ncoding.rpkm[grep("23.C", :
Reached total allocation of
Ok, that is why i have suspected.
Thanks for the clear explanation.
[]s
Cassiano
2014-04-09 18:37 GMT-03:00 Peter Langfelder peter.langfel...@gmail.com:
On Wed, Apr 9, 2014 at 11:27 AM, Cassiano dos Santos crn...@gmail.com
wrote:
I am testing a call to a C function from R, using .C
I am testing a call to a C function from R, using .C interface. The test
consists in passing a numeric vector to the C function with no entries,
dynamically allocates n positions, makes attributions and return the vector
to R.
I'm using Calloc from R.h. The prototype of the function is
type*
On Wed, Apr 9, 2014 at 11:27 AM, Cassiano dos Santos crn...@gmail.com wrote:
I am testing a call to a C function from R, using .C interface. The test
consists in passing a numeric vector to the C function with no entries,
dynamically allocates n positions, makes attributions and return the
Cassiano dos Santos crns13 at gmail.com writes:
I am testing a call to a C function from R, using .C interface. The test
consists in passing a numeric vector to the C function with no entries,
dynamically allocates n positions, makes attributions and return the
vector to R.
Asking on
dear R experts: I am curious again about R memory allocation strategies.
Consider an intentionally inefficient program:
ranmatme - function( lx, rx ) {
m - matrix(NA, nrow=lx, ncol=rx)
for (li in 1:rx) {
cat(\tLag i=, li, object size=, object.size(m), \n)
m[,li] - rnorm
; that
is the reason for the doubling.
On Mon, Jul 15, 2013 at 6:50 PM, ivo welch ivo.we...@anderson.ucla.eduwrote:
dear R experts: I am curious again about R memory allocation strategies.
Consider an intentionally inefficient program:
ranmatme - function( lx, rx ) {
m - matrix(NA, nrow=lx, ncol=rx
; that
is the reason for the doubling.
On Mon, Jul 15, 2013 at 6:50 PM, ivo welch ivo.we...@anderson.ucla.eduwrote:
dear R experts: I am curious again about R memory allocation strategies.
Consider an intentionally inefficient program:
ranmatme - function( lx, rx ) {
m - matrix(NA, nrow=lx, ncol
Dear All,
I am running R in a system with the following configuration
*Processor: Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
OS: Ubuntu X86_64 10.10
RAM: 24 GB*
The R session info is
*
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8
On 05/25/2012 06:29 AM, swaraj basu wrote:
Dear All,
I am running R in a system with the following configuration
*Processor: Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
OS: Ubuntu X86_64 10.10
RAM: 24 GB*
The R session info is
*
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu
Dear All,
I am running R in a system with the following configuration
*Processor: Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
OS: Ubuntu X86_64 10.10
RAM: 24 GB*
The R session info is
*
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8
Dear all, I know this problem was discussed many times in forum, however
unfortunately I could not find any way out for my own problem. Here I am
having Memory allocation problem while generating a lot of random number.
Here is my description:
rnorm(5*6000)
Error: cannot allocate vector of
32 bit windows has a memory limit of 2GB. Upgrading to a computer thats
less than 10 years old is the best path.
But short of that, if you're just generating random data, why not do it in
two or more pieces and combine them later?
mat.1 - matrix(rnorm(5*2000),nrow=5)
mat.2 -
8-02-2012, 22:22 (+0545); Christofer Bogaso escriu:
And the Session info is here:
sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: i386-pc-mingw32/i386 (32-bit)
Not an expert, but I think that 32-bit applications can only address
up to 2GB on Windows.
--
Bye,
Ernest
On Nov 23, 2011, at 10:42 AM, Marc Jekel wrote:
Dear R community,
I was observing a memory issue in R (latest 64bit R version running on a win
7 64 bit system) that made me curious.
I kept track of the memory f my PC allocated to R to calculate + keep several
objects in the workspace.
Dear R community,
I was observing a memory issue in R (latest 64bit R version running on a
win 7 64 bit system) that made me curious.
I kept track of the memory f my PC allocated to R to calculate + keep
several objects in the workspace. If I then save the workspace, close R,
and open the
Subject: [R] memory allocation in R
Dear R community,
I was observing a memory issue in R (latest 64bit R version running on
a
win 7 64 bit system) that made me curious.
I kept track of the memory f my PC allocated to R to calculate + keep
several objects in the workspace. If I then save
Hello, I am runnning a program on R with a big number of simulations and
I am getting the following error:
Error: no se puede ubicar un vector de tamaño 443.3 Mb
I don't understand why because when I check the memory status in my pc I get
the following:
memory.size()
[1] 676.3
Hi Felipe,
On Fri, Apr 8, 2011 at 7:54 PM, Luis Felipe Parra
felipe.pa...@quantil.com.co wrote:
Hello, I am runnning a program on R with a big number of simulations and
I am getting the following error:
Error: no se puede ubicar un vector de tamaño 443.3 Mb
I don't understand why because
: Lorenzo Cattarino
Sent: Wednesday, 3 November 2010 2:22 PM
To: 'David Winsemius'; 'Peter Langfelder'
Cc: r-help@r-project.org
Subject: RE: [R] memory allocation problem
Thanks for all your suggestions,
This is what I get after removing all the other (not useful) objects and
run my code:
getsizes
-Original Message-
From: David Winsemius [mailto:dwinsem...@comcast.net]
Sent: Wednesday, 3 November 2010 12:48 PM
To: Lorenzo Cattarino
Cc: r-help@r-project.org
Subject: Re: [R] memory allocation problem
Restart your computer. (Yeah, I know that what the help-desk always
says.)
Start R before
... imbue it.
- Jubal Early, Firefly
From:
Lorenzo Cattarino l.cattar...@uq.edu.au
To:
David Winsemius dwinsem...@comcast.net, Peter Langfelder
peter.langfel...@gmail.com
Cc:
r-help@r-project.org
Date:
11/03/2010 03:26 AM
Subject:
Re: [R] memory allocation problem
Sent by:
r-help-boun...@r
I forgot to mention that I am using windows 7 (64-bit) and the R version
2.11.1 (64-bit)
Thank you
Lorenzo
From: Lorenzo Cattarino
Sent: Wednesday, 3 November 2010 10:52 AM
To: r-help@r-project.org
Subject: memory allocation problem
Hi R users
I am trying to run a non linear
Hi R users
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
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
You have (almost) exhausted the 10GB you limited R to (that's what the
memory.size() tells you). Increase memory.limit (if you have more RAM,
use memory.limit(15000) for 15GB etc), or remove large data objects
from you session. Use rm(object), the issue garbage collection gc().
Sometimes garbage
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
Oops, I missed that you only have 4GB of memory... but since R is
apparently capable of using almost 10GB, either you actually have more
RAM, or the system is swapping some data to disk. Increasing memory
use in R might still help, but also may lead to a situation where the
system waits forever
On 02.10.2010 03:10, Peter Langfelder wrote:
Hi Mete,
I think you should look at the help for memory.limit. Try to set a
higher one, for example
memory.limit(16000)
(I think 16GB is what xenon will take).
But not too funny given you have only 8Gb in your machine.
So the answer probably
Hi Everyone,
I am getting the following error message
Error: cannot allocate vector of size 2.6 Gb
In addition: Warning messages:
1: In dim(res$res) = dim(bi) :
Reached total allocation of 8122Mb: see help(memory.size)
2: In dim(res$res) = dim(bi) :
Reached total allocation of 8122Mb: see
Hi Mete,
I think you should look at the help for memory.limit. Try to set a
higher one, for example
memory.limit(16000)
(I think 16GB is what xenon will take).
Peter
On Fri, Oct 1, 2010 at 6:02 PM, Mete Civelek mcive...@mednet.ucla.edu wrote:
Hi Everyone,
I am getting the following error
Dear all,
how can I use R on a 64-bit Windows Server 2003 machine (24GB RAM) with more
than 3GB of working memory and make full use of it.
I started R --max-mem-size=3G since I got the warning that larger values are
too large and ignored.
In R I got:
memory.size(max=FALSE)
[1] 10.5
On Wed, Jul 14, 2010 at 05:51:17PM +0200, will.ea...@gmx.net wrote:
Dear all,
how can I use R on a 64-bit Windows Server 2003 machine (24GB RAM) with more
than 3GB of working memory and make full use of it.
I started R --max-mem-size=3G since I got the warning that larger values are
too
Gabriel Margarido gramarga at gmail.com writes:
... I looked for a way to return the values
without copying (even tried Rmemprof), but without success. Any ideas?
...
I solved similar problems using the R.oo package, which emulates
pass-by-reference semantics in 'R'.
HTH
Keith
Hello everyone,
I have the following issue: one function generates a very big array (can be
more than 1 Gb) and returns a few variables, including this big one. Memory
allocation is OK while the function is running, but the final steps make
some copies that can be problematic. I looked for a way
On 1/16/2009 12:46 PM, Gabriel Margarido wrote:
Hello everyone,
I have the following issue: one function generates a very big array (can be
more than 1 Gb) and returns a few variables, including this big one. Memory
allocation is OK while the function is running, but the final steps make
some
Dear all,
I am trying to apply kmeans clusterring on a data file (size is about 300
Mb)
I read this file using
x=read.table('file path' , sep= )
then i do kmeans(x,25)
but the process stops after two minutes with an error :
Error: cannot allocate vector of size 907.3 Mb
when i read the
rami batal skrev:
Dear all,
I am trying to apply kmeans clusterring on a data file (size is about 300
Mb)
I read this file using
x=read.table('file path' , sep= )
then i do kmeans(x,25)
but the process stops after two minutes with an error :
Error: cannot allocate vector of size
Dear R users,
I am running a large loop over about 400 files. To outline generally,
the code reads in the initial data file, then uses lookup text files to
obtain more information before connecting to a SQL database using RODBC
and extracting more data. Finally all this is polar plotted.
My
See ?gc - it may help.
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Jamie Ledingham
Sent: Tuesday, August 12, 2008 9:16 AM
To: r-help@r-project.org
Subject: [R] Memory allocation problem
Dear R users,
I am running a large loop over about 400 files
Jamie Ledingham wrote:
becomes too much to handle by the time the loop reaches 170. Has anyone
had any experience of this problem before? Is it possible to 'wipe' R's
memory at the end of each loop - all results are plotted and saved or
written to text file at the end of each loop so this may
Following code bugs with Memory allocation failed: Copying Node error after
parsing n thousand files. I have included the main code(below) and
functions(after the main code).
I am not sure which lines are causing the copying Node which results in
memory failure. Please advise.
#Beginning
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