Ditto.

But isn't it just the result of the resulting object 'pa' containing the
substitutionArray slot (100 x 100 x 441 array of doubles)? Maybe
scoreOnly=TRUE is relevant in some cases?

b


On 2 November 2012 15:53, Wolfgang Huber <whuber@embl.de> wrote:

> 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@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
> >
> >
> >
> > --
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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