[BioC] cannot allocate vector of size 73 kb, in made4

[Kasper Daniel Hansen]

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)

<code starts> RAM usage: x
<allocate> RAM usage x + y:
<dosomething>
<allocate> RAM usage x+y+z
....
<code ends>

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