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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