From ml-it-r-devel at epigenomics.com  Thu Apr 17 21:34:45 2003
From: ml-it-r-devel at epigenomics.com (Matthias Burger)
Date: Thu Apr 17 20:34:58 2003
Subject: [Rd] R 1.7.0 installation problem: make check fails when using
 --with-lapack option
Message-ID: <news2mail-3E9EF3C5.2060803@epigenomics.com>



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

-- 
Matthias Burger

Bioinformatics R&D
Epigenomics AG                      www.epigenomics.com
Kleine Pr?sidentenstra?e 1          fax:   +49-30-24345-555
10178 Berlin Germany                phone: +49-30-24345-0


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