[BioC] BSgenome and R memory use

[Paul Leo]

Hi Martin,
Thanks for those tips; I think I can use them to get past this
bottle-neck.  

I too have become dependent on this nice package. 

Cheers
Paul
-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
Sent: Tuesday, 3 July 2007 9:32 PM
To: Paul Leo
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] BSgenome and R memory use

Hi Paul --

See class?BSgenome

I think what happens is that

> use.chromo <- Mmusculus[[chr.search[j]]]

causes the data to be loaded, and a 'view' to be created.

> rm(use.chromo)

removes the view, but does not unload the data. So you'll need to also

> unload(Mmusculus, chr.search[j])

I've found these packages very useful, thanks Herve!

Martin

"Paul Leo" <p.leo at uq.edu.au> writes:

> I have a bit of a problem with R running out of memory with BSgenome .
I
> have distilled it down to the bare bones. Basically I am just calling
up
> different mouse chromosomes and putting them into an object
> (use.chromo). I then immediately remove it with the simplistic idea
that
> this will free up the space that this object required. I always use
the
> same object and I do nothing with it. 
>
> The memory is rapidly depleted. I would love to know what tricks are
out
> there for cleaning up after removed objects. And in general what the
> origin of this behavior is....and ideas now to avoid it. 
>
> Until the loop below is stated I have enough memory to load any single
> mouse chromosome.
>
> Thanks 
> Paul
>
>  
> ### set up the test
> library(BSgenome.Mmusculus.UCSC.mm8)
> chromos<-c(1:19,"X","Y")
> chr.search<-paste("chr",chromos,sep="")
> #> chr.search
> # [1] "chr1"  "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"  "chr8"
> "chr9"  "chr10" "chr11" "chr12" "chr13"
> #[14] "chr14" "chr15" "chr16" "chr17" "chr18" "chr19" "chrX"  "chrY"
>
> ##### run the test
> k<-0
> for (i in 1:10){
> for (j in 1:length(chr.search)){
> use.chromo <- Mmusculus[[chr.search[j]]] 
> rm(use.chromo)
> k<-k+1 }   } # k is between 6 and 8 typically when this fails
> Error: cannot allocate vector of size 138.4 Mb
>
> ## note same behavior for R2.5 and earlier version of BS genome
> ## I am using the standard memory location for windows (1.5GB) I don't
> think increasing this will help much
>
> If you replace 
> use.chromo <- Mmusculus[[chr.search[j]]] 
> in the above loop with 
> p<- getSeq(Mmusculus, chr.search[j], 100,1000)
> a similar failure occurs. 
>
>
> sessionInfo()
> R version 2.6.0 Under development (unstable) (2007-06-26 r42066) 
> i386-pc-mingw32 
>
> locale:
>
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MON
>
ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets
methods
>
> [8] base     
>
> other attached packages:
> [1] BSgenome.Mmusculus.UCSC.mm8_1.3.0 BSgenome_1.5.0

> [3] Biobase_1.15.17                   Biostrings_2.5.11

>>
>
>
>  
>
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org