From chuckwhite8 at charter.net  Wed May  5 04:52:27 2010
From: chuckwhite8 at charter.net (Chuck White)
Date: Tue, 4 May 2010 22:52:27 -0400
Subject: [Rd] R 2.11.0 on RHEL5
In-Reply-To: <4BDE7B4B.3090505@statistik.tu-dortmund.de>
Message-ID: <20100504225227.56GSE.5692750.root@mp17>

Thank you for your response. I did look in the suggested manual under A.3.1.5 Shared BLAS.

Here are my steps: compiled R using
--with-readline=yes --enable-R-shlib=yes --enable-BLAS-shlib=yes --with-x=yes --prefix=/usr/local/R-2.11.0

Compiled LAPACK first and then ATLAS using http://www.scipy.org/Installing_SciPy/Linux#head-89e1f6afaa3314d98a22c79b063cceee2cc6313c   All the .so files have been copied to /usr/lib64

In /usr/local/R-2.11.0/lib64/R/lib, I renamed the .so files for blas and lapack and linked as
libRblas.so -> /usr/local/lib64/libf77blas.so
libRlapack.so -> /usr/local/lib64/liblapack.so

R does startup OK but when I do the following:
require(nlme)
fm1 <- nlme(height ~ SSasymp(age, Asym, R0, lrc), data = Loblolly, fixed = Asym + R0 + lrc ~ 1, random = Asym ~ 1, start = c(Asym = 103, R0 = -8.5, lrc = -3.3)) 

I get
/usr/local/R-2.11.0/lib64/R/bin/exec/R: symbol lookup error: /usr/local/R-2.11.0/lib64/R/lib/libRblas.so: undefined symbol: ATL_dgemm
This runs just fine without using the .so files which were built with R.

Can you please help?  Thanks.

---- Uwe Ligges <ligges at statistik.tu-dortmund.de> wrote: 
> This is explained in detail in the manual "R Installation and 
> Administration".
> 
> Best,
> Uwe Ligges
> 
> 
> On 03.05.2010 06:02, Chuck White wrote:
> > I have built lapack-3.2 and atlas3.8.3 for a RHEL5.3 VM.  The following files have been created -- libatlas (.a&  .so), libcblas (.a&  .so), libf77blas (.a&  .so), liblapack (.a&  .so), libptcblas (.a&  .so), libptf77blas (.a&  .so) and libstatatlas.a.
> >
> > When building R 2.11.0, I would like to be able to specify --with-blas and --with-lapack (and not use the ones which come with R). What is the syntax for that? Which of these libraries should I specify?
> >
> > Thanks.
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] R 2.11.0 on RHEL5
Chuck White