Hi Loren,

This might or might not help you out. Last time I helped teach a course on
bioconductor, many of the students in the course had a memory issue. The
solution that I came up with which helped everyone run their process was to
close all non-essential programs, particularly Firefox. While these students
were running linux with only 1 GB of RAM and not Mac OS with 2.5 GB ram,
this might be one thing to try.

Otherwise, I don't think buying RAM is the clear cut solution yet. There
have been quite a number of posts about allocation of memory, and maybe
these past posts can offer a better solution.

Cheers,
--Tony

PS - I don't think that people mean to be brusque when replying, but
people's tone can be easily misconstrued over e-mail. And here is my
criticism...you should really have a more descriptive title so this thread
can be easily parsed by others.

On Dec 8, 2007 6:00 AM, Loren Engrav <engrav@u.washington.edu> wrote:

> 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@jhsph.edu>
> > Date: Sat, 8 Dec 2007 00:23:10 -0500
> > To: Loren Engrav <engrav@u.washington.edu>
> > Cc: "bioconductor@stat.math.ethz.ch" <bioconductor@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@jhsph.edu>
> >>> Date: Sat, 8 Dec 2007 00:06:07 -0500
> >>> To: Loren Engrav <engrav@u.washington.edu>
> >>> Cc: "bioconductor@stat.math.ethz.ch" <bioconductor@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]]
> >>>>
> >>>> _______________________________________________
> >>>> Bioconductor mailing list
> >>>> Bioconductor@stat.math.ethz.ch
> >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>>> Search the archives:
> >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

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