[R] large data set, error: cannot allocate vector

Marc Schwartz (via MN) mschwartz at mn.rr.com
Tue May 9 23:00:48 CEST 2006

On Tue, 2006-05-09 at 15:35 -0500, Robert Citek wrote:
> On May 5, 2006, at 11:54 AM, Marc Schwartz (via MN) wrote:
> >> Robert Citek wrote:
> >>> $ uname -sorv ; rpm -q R ; R --version
> >>> Linux 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 GNU/ 
> >>> Linux
> >
> >           ^^^^^^^^^^^^^^^^^^^^
> > <snip>
> >
> > I might throw out one more pointer in addition to Uwe's comments  
> > above,
> > which _should_ not affect this issue, but as an FYI. Note that I said
> > "should not" versus "will not".
> >  ...
> > The current FC4 kernel release (noted above) has some issues with  
> > it at
> > present. A new kernel release version by Dave Jones, 2111, should  
> > be out
> > "any time now", but in the mean time, I would suggest updating your
> > kernel to version 2.6.16-1.2096smp and doing a full system update
> > generally.
> >
> > You may very well find that some behaviors (related and/or  
> > unrelated to
> > this issue) do change for the better.
> Thanks, Marc.  Upgraded:
> Linux 2.6.16-1.2096_FC4smp #1 SMP Wed Apr 19 15:51:25 EDT 2006 GNU/Linux
> Ran some simple tests and didn't notice any obvious improvement.   
> Nothing obviously broke, either, so that's good.


Happy to help.

One quick note, which is that the 2111 version of the kernel was
released using that number for FC5, but as 2108 for FC4. This fixes bugs
that cropped up in the 2107 version, which I referenced. I did not
experience them, but many others did, which seem to be hardware specific
to an extent.

So you can go ahead and upgrade to 2108 at your leisure.

The reason for mentioning the upgrades (not just the kernel, but system
wide) is that you never know what other issues may arise from
changes/updates in compilers, libraries and applications as bugs are
fixed. In addition and certainly non-trivial, are many security patches
that have been implemented since FC4 was released in June 2005.

One further aside to the thread more generally, is that you might want
to look at the R-admin manual relative to some of the pros/cons of
updating to 64 bit hardware, since this was referenced in the posts
today relative to expanding your RAM limits. It is available online


or as a PDF here:


The URLs above are using a U.S. mirror. Review section 8, "Choosing
between 32- and 64-bit builds".

There have also been many discussions on 32 vs. 64 bit by folks that you
will find in the r-help archives. Using:

  RSiteSearch("64 bit")

will get you almost 900 hits.



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