[Bioc-devel] serializing pairwise alignment objects

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 at 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 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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