Re: [R] memory.size help
At 13:27 31/08/2007, dxc13 wrote:
I keep getting the 'memory.size' error message when I run a program I have
been writing. It always it cannot allocate a vector of a certain size. I
believe the error comes in the code fragement below where I have multiple
arrays that could be taking up space. Does anyone know a good way around
this?
It is a bit hard without knowing the dimensions of the arrays but see below.
w1 - outer(xk$xk1, data[,x1], function(y,z) abs(z-y))
w2 - outer(xk$xk2, data[,x2], function(y,z) abs(z-y))
w1[w1 d1] - NA
w2[w2 d2] - NA
i1 - ifelse(!is.na(w1),yvals[col(w1)],NA)
i2 - ifelse(!is.na(w2),yvals[col(w2)],NA)
If I read this correctly after this point you no longer need w1 and
w2 so what happens if you remove them?
zk - numeric(nrow(xk)) #DEFININING AN EMPTY VECTOR TO HOLD ZK VALUES
for(x in 1:nrow(xk)) {
k - intersect(i1[x,], i2[x,])
zk[x] - mean(unlist(k), na.rm = TRUE)
}
xk$zk - zk
data - na.omit(xk)
--
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Michael Dewey
http://www.aghmed.fsnet.co.uk
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[R] memory.size help
I keep getting the 'memory.size' error message when I run a program I have
been writing. It always it cannot allocate a vector of a certain size. I
believe the error comes in the code fragement below where I have multiple
arrays that could be taking up space. Does anyone know a good way around
this?
w1 - outer(xk$xk1, data[,x1], function(y,z) abs(z-y))
w2 - outer(xk$xk2, data[,x2], function(y,z) abs(z-y))
w1[w1 d1] - NA
w2[w2 d2] - NA
i1 - ifelse(!is.na(w1),yvals[col(w1)],NA)
i2 - ifelse(!is.na(w2),yvals[col(w2)],NA)
zk - numeric(nrow(xk)) #DEFININING AN EMPTY VECTOR TO HOLD ZK VALUES
for(x in 1:nrow(xk)) {
k - intersect(i1[x,], i2[x,])
zk[x] - mean(unlist(k), na.rm = TRUE)
}
xk$zk - zk
data - na.omit(xk)
--
View this message in context:
http://www.nabble.com/memory.size-help-tf4359846.html#a12425401
Sent from the R help mailing list archive at Nabble.com.
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] memory.size help
You havn't said anithing about your OS and version. But basicly I means, that
you don't have enoigh RAM or swap memory aviable on your system. How large
dataset you have?
1. You can optimise your code. :)
or
2. You can just add more RAM to your system, or you can add more swap space on
your HDD. Work with data in swap will be really slow.
In linux OS you can add additional swap space, by these commmands:
2 GB file:
dd if=/dev/zero of=/swapfile1 bs=1024 count=2097152
mkswap /swapfile1
swapon /swapfile1
On Friday 31 August 2007 15:27:58 dxc13 wrote:
w1 - outer(xk$xk1, data[,x1], function(y,z) abs(z-y))
w2 - outer(xk$xk2, data[,x2], function(y,z) abs(z-y))
w1[w1 d1] - NA
w2[w2 d2] - NA
i1 - ifelse(!is.na(w1),yvals[col(w1)],NA)
i2 - ifelse(!is.na(w2),yvals[col(w2)],NA)
zk - numeric(nrow(xk)) #DEFININING AN EMPTY VECTOR TO HOLD ZK VALUES
for(x in 1:nrow(xk)) {
k - intersect(i1[x,], i2[x,])
zk[x] - mean(unlist(k), na.rm = TRUE)
}
xk$zk - zk
data - na.omit(xk)
--
Andris Jankevics
Assistant
Department of Medicinal Chemistry
Latvian Institute of Organic Synthesis
Aizkraukles 21, LV-1006, Riga, Latvia
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] memory.size help
I have 512 MB RAM with a 1.5 GHz processor. The dataset I am working with
increases with size with every iteration of the function that I am writing.
R can handle the input data which is about 10,000 records, and a single
iteration with 19,500 observations. After this, I get the memory.size()
error message.
I have only written 1 other R function so I am not too familiar with
optimizing code. Do you have any suggestions?
Andris Jankevics wrote:
You havn't said anithing about your OS and version. But basicly I means,
that
you don't have enoigh RAM or swap memory aviable on your system. How large
dataset you have?
1. You can optimise your code. :)
or
2. You can just add more RAM to your system, or you can add more swap
space on
your HDD. Work with data in swap will be really slow.
In linux OS you can add additional swap space, by these commmands:
2 GB file:
dd if=/dev/zero of=/swapfile1 bs=1024 count=2097152
mkswap /swapfile1
swapon /swapfile1
On Friday 31 August 2007 15:27:58 dxc13 wrote:
w1 - outer(xk$xk1, data[,x1], function(y,z) abs(z-y))
w2 - outer(xk$xk2, data[,x2], function(y,z) abs(z-y))
w1[w1 d1] - NA
w2[w2 d2] - NA
i1 - ifelse(!is.na(w1),yvals[col(w1)],NA)
i2 - ifelse(!is.na(w2),yvals[col(w2)],NA)
zk - numeric(nrow(xk)) #DEFININING AN EMPTY VECTOR TO HOLD ZK
VALUES
for(x in 1:nrow(xk)) {
k - intersect(i1[x,], i2[x,])
zk[x] - mean(unlist(k), na.rm = TRUE)
}
xk$zk - zk
data - na.omit(xk)
--
Andris Jankevics
Assistant
Department of Medicinal Chemistry
Latvian Institute of Organic Synthesis
Aizkraukles 21, LV-1006, Riga, Latvia
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
View this message in context:
http://www.nabble.com/memory.size-help-tf4359846.html#a12430698
Sent from the R help mailing list archive at Nabble.com.
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
