Message-ID: <AABAAB0B27AF5C418FE809F352FB7BA4083C9376@023-DB3MPN1-081.023d.mgd.msft.net>
Date: 2012-11-02T08:32:58Z
From: Hahne, Florian
Subject: [Bioc-devel] serializing pairwise alignment objects
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
--