[Bioc-devel] serializing pairwise alignment objects

Hahne, Florian florian.hahne at novartis.com
Fri Nov 2 09:32:58 CET 2012

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")
                 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:
35308996 bytes

Any idea what is going on here? Look like a memory leak to me.


R version 2.15.1 RC (2012-06-21 r59599)
Platform: i386-apple-darwin11.4.0/i386 (32-bit)

[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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