[BioC] Wow, what have I done

[Loren Engrav]

Ok
SessionInfo now returns

> sessionInfo()
R version 2.6.1 (2007-11-26)
powerpc-apple-darwin8.10.1

locale:
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] tools     stats     graphics  grDevices utils     datasets  methods
base     

other attached packages:
[1] affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.1
Biobase_1.16.1   

But I still get
> Gibran70 <- ReadAffy()
Error: cannot allocate vector of size 723.6 Mb
Although not big red messages which is not quite so hostile

I guess time to go to bed and in the AM buy some RAM

Thank you so much for the help

Engrav


> From: Benilton Carvalho <bcarvalh at jhsph.edu>
> Date: Sat, 8 Dec 2007 00:23:10 -0500
> To: Loren Engrav <engrav at u.washington.edu>
> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] Wow, what have I done
> 
> In that case, assuming that R-2.6.1 behaves just like R-2.6.0-patched
> in terms of memory management, you might want to define beforehand
> what you're going to be doing and, probably, use functions like
> justRMA().
> 
> b
> 
> On Dec 8, 2007, at 12:13 AM, Loren Engrav wrote:
> 
>> Thank you so much for the prompt help
>> 
>> Having been "scolded" for this before I now use sessionInfo which
>> returned
>> 
>>> sessionInfo()
>> R version 2.6.0 Patched (2007-11-09 r43408)
>> powerpc-apple-darwin8.10.1
>> 
>> locale:
>> 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] tools     stats     graphics  grDevices utils     datasets
>> methods
>> base
>> 
>> other attached packages:
>> [1] affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.1
>> Biobase_1.16.1
>> 
>> 
>>> From: Benilton Carvalho <bcarvalh at jhsph.edu>
>>> Date: Sat, 8 Dec 2007 00:06:07 -0500
>>> To: Loren Engrav <engrav at u.washington.edu>
>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>>> Subject: Re: [BioC] Wow, what have I done
>>> 
>>> I'd first make sure that you have the latest version (of R and the
>>> packages) installed...
>>> b
>>> 
>>> On Dec 7, 2007, at 11:59 PM, Loren Engrav wrote:
>>> 
>>>> So I enter
>>>> 
>>>>> GibranGlue70 <- ReadAffy() # to read in 70 .cel files
>>>> 
>>>> And I get this, all in bright red
>>>> 
>>>> Error: cannot allocate vector of size 723.6 Mb
>>>> R(22621,0xa000ed88) malloc: *** vm_allocate(size=758743040) failed
>>>> (error
>>>> code=3)
>>>> R(22621,0xa000ed88) malloc: *** error: can't allocate region
>>>> R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to
>>>> debug
>>>> R(22621,0xa000ed88) malloc: *** vm_allocate(size=758743040) failed
>>>> (error
>>>> code=3)
>>>> R(22621,0xa000ed88) malloc: *** error: can't allocate region
>>>> R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to
>>>> debug
>>>> 
>>>> I have 2.5 gb DDR SDRAM in the dual G5 Mac
>>>> 
>>>> Is the only answer, buy more RAM?
>>>> 
>>>> [[alternative HTML version deleted]]
>>>> 
>>>> _______________________________________________
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>> 
>> _______________________________________________
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