[Seqinr-forum] Memory leak?

[Darren Obbard]

Hi!

Not sure if this is an R problem or a seqinr problem or merely stupidity 
on my part, but I found it in a seqinr context using read.alignment()

my sesionInfo() is

R version 2.9.2 (2009-08-24)
i386-pc-mingw32

locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United 
Kingdom.1252;LC_MONETARY=English_United 
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] seqinr_2.0-7



and here is a fairly minimal example of the problem:
#--------------------------------------------------
require(seqinr)

#make a test file
write.fasta(seq=as.list(apply(matrix(rep("N",500000),nrow=100),1,paste,collapse="")),rep("seq",100),file="temp1.fas")

#run the loop until we run out of memory
counter<-0
memory.plot<-vector()
while(TRUE){
	temp<-read.alignment("temp1.fas",format="fasta")
	counter<-counter+1
}
counter
 > sessionInfo()
#cleanup
file.remove("temp.fas")
#--------------------------------------------------

-- 

Darren Obbard
Institute of Evolutionary Biology
Kings Buildings
University of Edinburgh, UK


The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.