Re: [Rd] First testing of R-2.0.0 alpha on Gentoo Linux

From: Prof Brian Ripley <>
Date: Tue 07 Sep 2004 - 17:14:41 EST

On 7 Sep 2004, Peter Dalgaard wrote:

> "M. Edward Borasky" <> 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,        
Professor of Applied Statistics,
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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