Hi,
Looks like Benilton is right:
> slotNames(pa)
[1] "pattern" "subject" "type"
[4] "score" "substitutionArray" "gapOpening"
[7] "gapExtension"
> sapply(slotNames(pa), function(sname) object.size(slot(pa, sname)))
pattern subject type score
17056 17056 96 48
substitutionArray gapOpening gapExtension
35295336 48 48
I'm not sure why the substitutionArray would need to be stored in the
returned object (what downstream method use it?). Would need to check.
H.
On 11/02/2012 09:41 AM, Benilton Carvalho wrote:
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 <whu...@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.ha...@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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Program in Computational Biology
Division of Public Health Sciences
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