Question: cannot allocate vector of size 73 kb, in made4
0
12.0 years ago by
Amin Moghaddasi130 wrote:
Dear All, This has been asked several times before in different threads, However this error seems to be a 32bit windows OS memory usage related to R. Although I am using Dual Core Processor with 2GB of RAM running kubuntu Gutsy version 7.10, However I've got the same error "can not allocate vector of size 73 kb" as well. I'm not sure whether this is related to the specific function/package that I'm using, since I've got exactly the same size of 73 kb, on two different machines! (the above machine, and the other with 4GB RAM !!) The function that I wanted to use is "cia" in "made4" package version 1.12. Basically what I've done is: > data1723 <- read.csv('1723.csv',header=TRUE,row.names="geneNames") > data2224 <- read.csv('2224.csv',header=TRUE,row.names="geneNames") > coin <- cia(data1723,data2224) Error: cannot allocate vector of size 73 Kb > > dim(data1723) [1] 9335 24 > dim(data2224) [1] 9335 24 > sessionInfo() R version 2.6.0 (2007-10-03) i486-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] made4_1.12.1 ade4_1.4-5 loaded via a namespace (and not attached): [1] rcompgen_0.1-17 > traceback() 4: unlist(vlist, recursive = FALSE, use.names = FALSE) 3: data.frame(tabcoiner) 2: coinertia(t.dudi(coa1), t.dudi(coa2), nf = cia.nf, scan = cia.scan, ...) 1: cia(data1723, data2224) --- $free -m total used free shared buffers cached Mem: 3424 3320 103 0 5 115 -/+ buffers/cache: 3200 223 Swap: 6000 81 5919 Any sugestions are appreciated, Regards, Amin. • 734 views ADD COMMENTlink modified 12.0 years ago by Kasper Daniel Hansen6.4k • written 12.0 years ago by Amin Moghaddasi130 Answer: cannot allocate vector of size 73 kb, in made4 0 12.0 years ago by United States Kasper Daniel Hansen6.4k wrote: Whenever you get a message like this you have run out of ram. You cannot really say how much ram you needed, because what happens is really something like this (pseudocode)  RAM usage: x <allocate> RAM usage x + y: <dosomething> <allocate> RAM usage x+y+z .... at some point the code tries to allocate a vector and R runs out of memory. The size you get (73kb in the post) is just the last straw that breaks the camel's back so to say. If you are running out of ram there are several possibilites: 1) get more RAM. But this will only help if you use a OS that can make R use more RAM. Say you are running windows XP and you buy 32 GB ram. That will not help you, because a single process can only use I think 2 GB. 2) get more RAM and a 64 bit OS that actually makes it possible to use the RAM 3) rewrite the code to get around memory limitations 3) will only work for some usages. But in many cases people do not pay much attention to RAM usage when they program, so sometimes it is easy to cut the usage down. I have no experience with cia at all. It could be that your dataset is imply to big to use this function. Dual cores does not help you. Kasper On Nov 6, 2007, at 12:15 PM, Amin Moghaddasi wrote: > Dear All, > > This has been asked several times before in different threads, However > this error seems to be a 32bit windows OS memory usage related to R. > > Although I am using Dual Core Processor with 2GB of RAM running > kubuntu > Gutsy version 7.10, However I've got the same error "can not allocate > vector of size 73 kb" as well. I'm not sure whether this is related to > the specific function/package that I'm using, since I've got > exactly the > same size of 73 kb, on two different machines! (the above machine, and > the other with 4GB RAM !!) > The function that I wanted to use is "cia" in "made4" package version > 1.12. > Basically what I've done is: > >> data1723 <- read.csv('1723.csv',header=TRUE,row.names="geneNames") >> data2224 <- read.csv('2224.csv',header=TRUE,row.names="geneNames") >> coin <- cia(data1723,data2224) > Error: cannot allocate vector of size 73 Kb >> >> dim(data1723) > [1] 9335 24 >> dim(data2224) > [1] 9335 24 > >> sessionInfo() > R version 2.6.0 (2007-10-03) > i486-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US > .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. > UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 > ;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] made4_1.12.1 ade4_1.4-5 > > loaded via a namespace (and not attached): > [1] rcompgen_0.1-17 >> traceback() > 4: unlist(vlist, recursive = FALSE, use.names = FALSE) > 3: data.frame(tabcoiner) > 2: coinertia(t.dudi(coa1), t.dudi(coa2), nf = cia.nf, scan = cia.scan, > ...) > 1: cia(data1723, data2224) > --- > >$ free -m > total used free shared buffers > cached > Mem: 3424 3320 103 0 5 > 115 > -/+ buffers/cache: 3200 223 > Swap: 6000 81 5919 > > > Any sugestions are appreciated, > Regards, > Amin. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor 
ADD COMMENTlink written 12.0 years ago by Kasper Daniel Hansen6.4k
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