From SheltonS at stemcell.ucsf.edu  Wed Aug 21 17:17:55 2013
From: SheltonS at stemcell.ucsf.edu (Shelton, Samuel)
Date: Wed, 21 Aug 2013 15:17:55 +0000
Subject: [Rd] Problem with R >3.0.0
In-Reply-To: <E7CFD001-DE7D-4534-B1A2-8C5E1F5613BB@gmail.com>
References: <CE38EC7A.1872F%sheltons@stemcell.ucsf.edu>,
	<E7CFD001-DE7D-4534-B1A2-8C5E1F5613BB@gmail.com>
Message-ID: <8A011F8D-BFB0-45A5-85DC-8B6DB1A0BF6B@stemcell.ucsf.edu>

Thanks for looking into this for me.

I made a mistake with the version of Osx I was using it is actually 10.8.4 mountain lion. Interestingly it was doing the same on this particular iMac with snow leopard and that was the reason that I upgraded it to mountain lion. I found the same problem with v3.0.0 and with 3.0.1 both with snow leopard and mountain lion.  2.15.2 which is the same verion that we use on our cluster did not give this behaviour on either snow leopard or mountain lion.

Please let me know if you want me to do any more testing as I have access to machines with lots of ram.

Sam

Sent from my iPad

On Aug 21, 2013, at 5:46 AM, "peter dalgaard" <pdalgd at gmail.com> wrote:

> 
> On Aug 20, 2013, at 19:42 , Shelton, Samuel wrote:
> 
>> Hi all,
>> 
>> Thanks for getting back to me. We would like to move over to v3.0.0 on our
>> cluster so that we can build matrices larger than 46300*46300 (limit in R
>> <3.0.0)
>> but so far we can't get things to work with R v3.0.0 and higher. I am
>> trying to trouble shoot at the moment and I am now thinking that the
>> problem is actually with the diag function that has been rewritten in
>> version 3.0.0. 
>> 
>> 
>> The problem is definitely with the diag function and it does not occur on
>> smaller matrices (20000*20000) and I think it maybe a bug.
>> This illustrates the problem:
>> 
>> This was done on an iMac i5 with OSX 10.8.5 16GB Ram and with R 3.0.1 (but
>> I do see the same for 3.0.0). This does not occur when I run it with R
>> 2.15.2. 
>> 
> 
> 
> Thanks. I can condense this to 
> 
>> M <- matrix(1,23170,23170) ; diag(M) <- 0 ; range(colSums(M))
> [1] 23169 23169
>> M <- matrix(1,23171,23171) ; diag(M) <- 0 ; range(colSums(M))
> [1]     0 23170
> 
> and the fact that 2^14.5 is 23170.48 is not likely to be a coincidence...
> 
> It is only happening with some of my builds, though. In particular, my MacPorts build of 3.0.1 does not have the problem on Snow Leopard, nor does the CRAN build of 3.0.0, still on Snow Leopard. It takes forever to check on a 4GB machine....
> 
> -- 
> Peter Dalgaard, Professor
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com
> 



[Rd] Problem with R >3.0.0
Shelton, Samuel