Inlined below:
On Sun, Nov 14, 2010 at 12:46 PM, Steve Lianoglou <
[email protected]> wrote:
> Hi Steven,
>
> Are you still having problems?
>
yes, it's pretty bad. For example,I launch R . At the start up R consumes
about 50-60mb.
I then merely open a document, an existing script, memory usage jumps to
500mb.
I then select a couple lines to copy. Memory runs past 1gb and the system
freezes for minutes at a time. Then magically the memory drops back down to
50 mb. This happened with R.2.11 and now with R 2.12.
>
> I'd be surprised if R-2.12 itself has anything to do with the problems
> you're seeing, but assuming 2.11 is still on your system, you can
> switch to it easily by using Rswitch, that you can find here:
>
> http://r.research.att.com/#other
>
> It assumes 2.11 was installed via the normal R installers, ie. it lives in:
>
> /Library/Frameworks/R.framework/Versions/2.11
>
> A few Q's for you:
>
> (1) Did you reinstall your R libraries for 2.12 from scratch (good
> idea) , or did you copy them over from your 2.11 install (bad idea)
>
I downloaded the 2.12 package and installed it. 2.11 is still in place
>
> (2) Are you using R from R.app or from the terminal?
>
R.app
>
> (2a) When you run are from the Terminal, does it still exhibit this
> behavior?
> (2b) How about if you start R with the --vanilla flag?, eg:
>
> $ R --vanilla
>
I'll give that a try and let you know.
>
> If you want to completely uninstall R 2.12 and start from scratch, you
> can do that from the terminal, too:
>
> $ sudo rm -Rf /Library/Frameworks/R.framework/Versions/2.12
>
Great. My other issue is that a library I depend on "ncdf" worked under
R.2.11 but it's absent now and it looks like the upgrade to that package
isnt on cran for the Mac anymore.
>
> Hope that helps,
> -steve
>
> btw - I don't think "MAC" needs to be capitalized ... it's not an acronym
> ;-)
>
> On Fri, Nov 12, 2010 at 3:50 PM, steven mosher
> wrote:
> > I recently noticed that R was having memory "race" condition on my MAC.
> At
> > start up it would race to 1.3GB of memory used. Just on start up. For no
> > apparent reason. Then it would release memory and fall back down to
> 50-60MB.
> > Upon opening any window to edit old files or
> > start a new one, the race would come back. programs that used to execute
> in
> > short periods would take forever. Often not completing after hours.
> >
> > So:
> >
> > 1. did did a MAC system update ( Leopard)
> > 2. installed R 2.12
> > 3. X11 gets clobbered so I had to reinstall that.
> > 4. RGDAL had to be reinstalled but I was able to make that work after
> some
> > time.
> >
> > Now raster programs that worked an hour ago are broken and I found out
> that
> > ncdf is not available yet.
> >
> > What's the simplest way to revert to R 2.11 and diagnose the memory race
> I
> > seem to be having.
> >
> >[[alternative HTML version deleted]]
> >
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> > [email protected]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
>
>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
> | Memorial Sloan-Kettering Cancer Center
> | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
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