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$zk <- zk
data <- na.omit(xk)
--
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You havn't said anithing about your OS and version. But basicly I means, that you don't have enoigh RAM or swap memory aviable on your system. How large dataset you have? 1. You can optimise your code. :) or 2. You can just add more RAM to your system, or you can add more swap space on your HDD. Work with data in swap will be really slow. In linux OS you can add additional swap space, by these commmands: 2 GB file: dd if=/dev/zero of=/swapfile1 bs=1024 count=2097152 mkswap /swapfile1 swapon /swapfile1 On Friday 31 August 2007 15:27:58 dxc13 wrote:> w1 <- outer(xk$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
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) >-- >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.Michael Dewey http://www.aghmed.fsnet.co.uk