From ripley at stats.ox.ac.uk  Thu Jul 12 21:17:44 2007
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Thu, 12 Jul 2007 20:17:44 +0100 (BST)
Subject: [Rd] cleanup and Makevars
In-Reply-To: <46967C8B.5000300@cimr.cam.ac.uk>
References: <A153F980-E93F-4623-B097-E7635151386B@stat.berkeley.edu>
	<Pine.LNX.4.64.0707100553350.16628@gannet.stats.ox.ac.uk>
	<637BDDED-F9CD-48D1-A0C1-D982AAA9DA29@stat.Berkeley.EDU>
	<46967C8B.5000300@cimr.cam.ac.uk>
Message-ID: <Pine.LNX.4.64.0707122016210.26523@gannet.stats.ox.ac.uk>

On Thu, 12 Jul 2007, Hin-Tak Leung wrote:

> Kasper Daniel Hansen wrote:
>> On Jul 11, 2007, at 9:30 AM, Prof Brian Ripley wrote:
> <snipped>
>>>> The full Makevars file:
>>>> 
>>>> MYCXXFLAGS=-O0
>>> You do realize that is highly non-portable?
>> 
>> Yes, but I do not know of any other way to downgrade the optimization 
>> level. The SDK I am using breaks (due to memory alignment issues if a 
>> specific optimization flag for GCC is include - the flag is certainly 
>> implied by -O2 and as far as I recall also -O1). I guess the solution  is 
>> to switch to an autoconfigure script. The main reason for not  doing this 
>> is 1) time and actually more 2) the fact that the SDK does  not come with 
>> an ac script.
>> 
>> Thanks for the feedback, Kasper
> <snipped>
>
> I think I probably know about the breakage - gcc 4.x mis-compiles
> the Affymetrix toolkit at the default optimization (-02) shipped with the 
> toolkit. (Prof Ripley's comment was spot-on - why the reluctance
> to just call it the Affymetrix toolkit bundled with the bioconductor
> package affyparser?). I narrowed it down to the strict-aliasing
> option... try '-O2 -fno-strict-aliasing' - it is not portable, but it
> works around the funny way some part of the affy toolkit (actually one
> particular file) is written.
>
> I did report it in the Affy forum and also directly to my Affymetrix
> dev contacts about a year ago; gcc 4 is the default on the mac these
> days, I think?
>
> On a related issue, I have some annoyance with cross-compiling leaving behind 
> *.o files (and *.d, etc) which get in the way of native
> compile and vice versa, and I have been wondering if there is a
> recommended solution? What I am currently doing is to have a

Hopefully the --clean options to INSTALL and SHLIB in R-devel will help.
If they don't examples of what is needed will help improve.

> "Makefile.utils" (I don't want or need a proper Makefile), and do
> 'make -f Makefile.utils clean' when I need to clean up - it is better
> than typing
>  rm -f  *.o *.so *~ *.rc *.d *.dll Makedeps *.def
>
> (particularly with bash's file completion, all I am typing is
> 'make -f M<tab>f<tab> clean' to clean up). I am sure somebody will laugh
> at this...
>
> Hin-Tak
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] cleanup and Makevars
Prof Brian Ripley