On 11/2/12 7:02 PM, "Herv? Pag?s" <hpages at fhcrc.org> wrote:
>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 <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
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>> _______________________________________________
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>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
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>>
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>
>--
>Herv? Pag?s
>
>Program in Computational Biology
>Division of Public Health Sciences
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>
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