From bates at stat.wisc.edu  Thu Apr 17 15:07:19 2003
From: bates at stat.wisc.edu (Douglas Bates)
Date: Thu Apr 17 21:07:36 2003
Subject: [Rd] R 1.7.0 installation problem: make check fails when using
	--with-lapack option
In-Reply-To: <news2mail-3E9EF3C5.2060803@epigenomics.com>
References: <news2mail-3E9EF3C5.2060803@epigenomics.com>
Message-ID: <6ry929eye0.fsf@bates4.stat.wisc.edu>

Matthias Burger <ml-it-r-devel@epigenomics.com> writes:

> Greetings,
> 
> compiling R 1.7.0 with gcc 3.1.1 on Debain Linux (woody stable) with
> the configure option --with-lapack works but make check fails in test
> base-R with the message
> 
> 
> [...]
>  > kappa(x1 <- cbind(1,1:10))# 15.71
> [1] 15.70590
>  > kappa(x1, exact = TRUE)        # 13.68
> [1] 13.67903
>  > kappa(x2 <- cbind(x1,2:11))# high! [x2 is singular!]
> [1] 8.351867e+16
>  >
>  > hilbert <- function(n) { i <- 1:n; 1 / outer(i - 1, i, "+") }
>  > sv9 <- svd(h9 <- hilbert(9))$ d
>  > kappa(h9)# pretty high!
> [1] 728289149562
>  > kappa(h9, exact = TRUE) == max(sv9) / min(sv9)
> Error in La.svd(x, nu, nv, method) : LAPACK routine DGEBRD gave error code -10
> Execution halted
> 
> As I understand from the configure output (and config.status) R used
> the -L/R_HOME/bin -lRlapack
> 
> but this seemed to have built ok.
> 
> compiling anew after configure with the same option set but without
> --with-lapack make check yields not error test base-R
> 
> 
> Is this a known problem with gcc 3.1.1? Or my configure call configuration?
> There are lapack dyn libs installed for my system so I thought
> configure would find those - did I make a mistake in the configure
> options?
> 
> 
> Any hints would be very wellcome.
> 
> 
> Just now, for testing reconfigured (after make clean) and recompiled
> with gcc 2.95.4 using the --with-lapack option and failed make check
> again (same error). So what could be wrong with the lapack option?
> 
> 
> 
> Regards,
> 
>     Matthias
> 
> 
> 
> details:
> 
> export CC=gcc-3.1 CXX=g++-3.1
> 
>    ./configure --prefix=/mnt/local/R/R-1.7.0-gcc-3.1.1
> --enable-R-profiling=yes --enable-R-shlib=yes --with-f77
> --with-blas=yes --with-lapack=yes --with-readline=yes
> --with-tcltk=/usr/include/tcl8.3
> --with-tcl-config=/usr/lib/tcl8.3/tclConfig.sh
> --with-tk-config=/usr/lib/tk8.3/tkConfig.sh --enable-shared --with-pic
> --with-x
> 
> --with-gnome --with-gnome-includes=/usr/include/gnome-1.0
> --with-recommended-packages --with-aqua=yes  --with-libpng=yes
> --with-jpeglib=yes --with-zlib=yes --with-bzlib=yes --with-pcre=yes
> --with-libglade-config=/usr/bin/libglade-config
> 
> 
>    configure output:
> 
>    R is now configured for i686-pc-linux-gnu
> 
>    Source directory:          .
>    Installation directory:    /mnt/local/R/R-1.7.0-gcc-3.1.1
> 
>    C compiler:                gcc-3.1 -D__NO_MATH_INLINES -mieee-fp -g -O2
>    C++ compiler:              g++-3.1 -mieee-fp -g -O2
>    Fortran compiler:          g77 -mieee-fp -g -O2
> 
>    Interfaces supported:      X11, gnome, tcltk
>    External libraries:        readline, BLAS(ATLAS), LAPACK(generic)
>    Additional capabilities:   PNG, JPEG, bzip2, PCRE
>    Options enabled:           shared library, R profiling
> 
>    Recommended packages:      no

Very peculiar.  I just checked the machine where I compiled the
R-1.7.0 Debian packages for the stable distribution.  During the
Debian package build we do run 'make check' and that succeeded on that
machine.

Now I get the peculiar situation that, with h9 the 9x9 Hilbert matrix,
I can successfully run

svd(h9)
svd(h9, nu = 0)
svd(h9, nv = 0)

but

svd(h9, nu = 0, nv = 0)

fails with the error that you quote.

I compiled these packages with g77-3.0 for the Fortran compiler.  Are
there known problems with that?

On another machine running Debian testing and using the gcc-3.2
compiler suite the tests pass.


[Rd] R 1.7.0 installation problem: make check fails when using --with-lapack option
Douglas Bates