From ripley at stats.ox.ac.uk  Tue Sep  7 09:14:41 2004
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Tue Sep  7 09:14:47 2004
Subject: [Rd] First testing of R-2.0.0 alpha on Gentoo Linux
In-Reply-To: <x2n0028tbz.fsf@biostat.ku.dk>
Message-ID: <Pine.LNX.4.44.0409070806510.8318-100000@gannet.stats>

On 7 Sep 2004, Peter Dalgaard wrote:

> "M. Edward Borasky" <znmeb@aracnet.com> writes:
> 
> > I just got R-2.0.0 alpha running on my Gentoo Linux system. The only
> > issue I had was that if I do "--with-lapack" in the "configure", "make
> > check" fails very early. 

It would have been helpful to say where, exactly.

> Once I removed that option, "make check-all"
> > passed. I have both "blas-atlas" and "lapack-atlas" installed on my
> > system. The Atlas version is 3.6.0.
> 
> Hmm, but would the linker know where to find them? Also, there could
> be an issue with dynamic vs. static libraries. Any configure experts
> around? 

(Well, I wrote that part of configure, amongst others.) R-admin does warn
against using --with-lapack:

  Provision is made for using an external LAPACK library, principally to
  cope with BLAS libraries which contain a copy of LAPACK ...

Note that lapack-atlas is probably not a complete lapack, and if it is, it 
may not be bug-fixed ...

   If you do use @option{--with-lapack}, be aware of potential problems
   with bugs in the LAPACK 3.0 sources (or in the posted corrections to 
   those sources).

So all I can conclude from this is that Gentoo's libraries are not 
sufficient.

When I do this, I have to be very careful how I build LAPACK, using
-fforce-store where R does.  It then works but I see negligible 
performance boost (Goto's BLAS is better than ATLAS, anyway).

-- 
Brian D. Ripley,                  ripley@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] First testing of R-2.0.0 alpha on Gentoo Linux
Prof Brian Ripley