From bates at stat.wisc.edu  Fri May 14 15:00:52 2010
From: bates at stat.wisc.edu (Douglas Bates)
Date: Fri, 14 May 2010 08:00:52 -0500
Subject: [Rd] Compiling R with ATLAS
In-Reply-To: <AANLkTin1X624rbBUEZg5GiJU6Xam79NhRRjFPqhSuuuI@mail.gmail.com>
References: <AANLkTin1X624rbBUEZg5GiJU6Xam79NhRRjFPqhSuuuI@mail.gmail.com>
Message-ID: <AANLkTinXKRyabRrYK4J5Xf3h_DOkjQaN8AEtayGoFZZS@mail.gmail.com>

There is a Debian/Ubuntu specific list, R-SIG-Debian at R-project.org,
which I am cc:'ing on this reply, that is a better location for this
discussion.

It appears that you may be going about things the hard way.  There are
Ubuntu packages for atlas and for R that can handle all of this for
you.  Take a look at http://cran.r-project.org/bin/linux/ubuntu for
information on how to get started.  It will probably be much easier to
install the pre-compiled packages first and worry about compilation
for customization later.

On Thu, May 13, 2010 at 11:16 PM, Avraham Adler <avraham.adler at gmail.com> wrote:
> Hello. I know almost nothing about Linux, so I apologize if the answer to
> this is obvious.
>
> I am trying to compile R with ATLAS (successfully compiled 3.9.24 on Ubuntu
> 10.04 64 bit). I configured with:
>
> ./configure --enable-R-shlib --enable-BLAS-shlib
> --with-blas="-L/usr/local/atlas/lib -lf77blas -latlas"
> --with-lapack="-L/usr/local/atlaslib -llapack -lcblas" --with-x
>
> and I get this error (from config.log):
>
> configure:28566: checking for dgemm_ in -L/usr/local/atlas/lib -lf77blas
> -latlas
> configure:28587: gcc -std=gnu99 -o conftest -g -O2 -fpic
> -I/usr/local/include ?-L/usr/local/lib64 conftest.c -L/usr/local/atlas/lib
> -lf77blas -latlas ?-lgfortran -lm -ldl -lm ?>&5
> conftest.c: In function 'main':
> conftest.c:193: warning: implicit declaration of function 'dgemm_'
> /usr/local/atlas/lib/libf77blas.so: undefined reference to
> `atl_f77wrap_zger2u_'
> /usr/local/atlas/lib/libf77blas.so: undefined reference to
> `atl_f77wrap_cger2c_'
> /usr/local/atlas/lib/libf77blas.so: undefined reference to
> `atl_f77wrap_zger2c_'
> /usr/local/atlas/lib/libf77blas.so: undefined reference to
> `atl_f77wrap_cger2u_'
> collect2: ld returned 1 exit status
> configure:28587: $? = 1
>
> I found the following e-mail in the archives <
> http://www.mail-archive.com/r-devel at r-project.org/msg16853.html>, but it has
> a different error, and the suggestion of switching out the BLAS later does
> not seem to apply to ATLAS which requires two files, I think.
>
> Any advice would be very appreciated.
>
> Thank you.
>
> ? ? ? ?[[alternative HTML version deleted]]
>
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>



[Rd] Compiling R with ATLAS
Douglas Bates