[Bioc-devel] serializing pairwise alignment objects

[Wolfgang Huber]

Hi,

I can reproduce this on more recent versions of everything:

> sessionInfo()
R Under development (unstable) (2012-10-31 r61057)
Platform: x86_64-apple-darwin12.2.0/x86_64 (64-bit)

locale:
[1] C

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

other attached packages:
[1] Biostrings_2.27.5  IRanges_1.17.7     BiocGenerics_0.5.1 fortunes_1.5-0    

loaded via a namespace (and not attached):
[1] stats4_2.16.0

Best wishes
	Wolfgang

Il giorno Nov 2, 2012, alle ore 9:32 AM, "Hahne, Florian" <florian.hahne at novartis.com> ha scritto:

> Hi all,
> I just realized that serialized PairwiseAlignmentsSingleSubject objects
> grow ridiculously large:
> 
> x <- "xxxabcdefghijklmnopqyyy"
> y <- "abcdhijkzzzzlmnpqr"
> pa <- pairwiseAlignment(x,y)
> save(pa, file="~/tmp/pa.rda")
> file.info("~/tmp/pa.rda")
>                 size isdir mode               mtime               ctime
> ~/tmp/pa.rda 22651025 FALSE  644 2012-11-02 09:23:09 2012-11-02 09:23:09
>                           atime   uid   gid    uname   grname
> ~/tmp/pa.rda 2012-11-02 09:23:07 11281 11281 hahnefl1 hahnefl1
> 
> 
> 
> 22 MB for this trivial alignment seems to be a little excessive.
> 
> Interestingly, the object itself has a quite impressive memory footprint:
> object.size(pa)
> 35308996 bytes
> 
> 
> Any idea what is going on here? Look like a memory leak to me.
> 
> 
> Florian
> 
> sessionInfo()
> R version 2.15.1 RC (2012-06-21 r59599)
> Platform: i386-apple-darwin11.4.0/i386 (32-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] Biostrings_2.26.2   IRanges_1.16.2      BiocGenerics_0.4.0
> [4] BiocInstaller_1.8.2
> 
> loaded via a namespace (and not attached):
> [1] parallel_2.15.1 stats4_2.15.1   tools_2.15.1
> 
> 
> 
> -- 
> 
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