From ml-it-r-devel at epigenomics.com  Tue Apr 22 20:38:11 2003
From: ml-it-r-devel at epigenomics.com (Matthias Burger)
Date: Tue Apr 22 19:38:24 2003
Subject: [Rd] R 1.7.0 installation problem: make check fails when using
   --with-lapack option
References: <news2mail-3E9EF3C5.2060803@epigenomics.com>
	<6ry929eye0.fsf@bates4.stat.wisc.edu>
	<20030417191950.GA12963@sonny.eddelbuettel.com>
	<16033.38796.844040.879450@mithrandir.hornik.net>
Message-ID: <news2mail-3EA57E03.5090006@epigenomics.com>


Hi again,

first I'd like to thank you for the prompt replies and insights.

So here is my next attempt log:
After some conversation with my local sys admins I convinced them to install gcc 
3.2.2 (also g++ and g77 for that version) compiled for Debain woody stable (!) 
as that is our site wide system setup.

And yes I simply had forgotten to set the correct g77 version (thanks to Dirk 
for pointing this out).

As we have now one central installation point for R (and not on each host 
individually) I cannot use the Debian package system I believe. Even if so I do 
not have root access and thus have to stick to comile myself from src.

So after some experimenting my host now is configured with packages
blas  &  blas-dev (Version: 1.1-9)
lapack2 & lapack2-dev (Version: 3.0.20000531a-18)
and
atlas2-sse2 & atlas2-sse2-dev (Version: 3.2.1ln-7)

exporting the gcc variables, make distclean

configure (see below)

make
runs through but
make check
fails with the same error in base.R as reported earlier.

ldd bin/R.bin reports

kuhn burger 243 (R/R-1.7.0-inst): ldd bin/R.bin
         libblas.so.2 => /usr/lib/sse2/atlas/libblas.so.2 (0x40027000
         libg2c.so.0 => /usr/lib/libg2c.so.0 (0x403fd000)
         libm.so.6 => /lib/libm.so.6 (0x40419000)
         libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x4043b000)
         libpcre.so.3 => /usr/lib/libpcre.so.3 (0x40443000)
         libbz2.so.1.0 => /usr/lib/libbz2.so.1.0 (0x4044c000)
         libz.so.1 => /usr/lib/libz.so.1 (0x4045c000)
         libreadline.so.4 => /lib/libreadline.so.4 (0x4046c000)
         libdl.so.2 => /lib/libdl.so.2 (0x40492000)
         libncurses.so.5 => /lib/libncurses.so.5 (0x40496000)
         libc.so.6 => /lib/libc.so.6 (0x404d4000)
         /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000)

  so it seems to find the libblas
but starting R and doing the same I get

 >system("ldd bin/R.bin")
         libblas.so.2 => /usr/lib/gcc-lib/i386-linux/3.2.2/../../../libblas.so.2 
(0x40016000)
         libg2c.so.0 => /usr/lib/gcc-lib/i386-linux/3.2.2/../../../libg2c.so.0 
(0x40079000)
         libm.so.6 => /lib/libm.so.6 (0x400a6000)
[...]

even if I set
export LD_LIBRARY_PATH=/usr/lib/sse2/atlas:$LD_LIBRARY_PATH
I get the same picture.

Now I have no further knowledge how to check & persuade the run time linker to 
pick up the correct libs. In any case I believ this to be the cause of the 
failure or am I grossly mistaken?

Any suggestions what I could try next (or just leave it and  waive lapack support) ?


Regards,

   Matthias



details:

kuhn burger 249 (R/R-1.7.0-inst): /usr/bin/gcc-3.2 --version
gcc-3.2 (GCC) 3.2.2
Copyright (C) 2002 Free Software Foundation, Inc.


    ./configure --prefix=/mnt/local/R/R-1.7.0-gcc-3.2.2-atlas2-sse2 
--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=/mnt/local/R/R-1.7.0-recommended-inst 
--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



R is now configured for i686-pc-linux-gnu

   Source directory:          .
   Installation directory:    /mnt/local/R/R-1.7.0-gcc-3.2.2-atlas2-sse2

   C compiler:                /usr/bin/gcc-3.2 -D__NO_MATH_INLINES -mieee-fp -g -O2
   C++ compiler:              /usr/bin/g++-3.2 -mieee-fp -g -O2
   Fortran compiler:          /usr/bin/g77-3.2 -mieee-fp -g -O2

   Interfaces supported:      X11, gnome, tcltk
   External libraries:        readline, BLAS(generic), LAPACK(generic)
   Additional capabilities:   PNG, JPEG, bzip2, PCRE
   Options enabled:           shared library, R profiling

   Recommended packages:      no

Kurt Hornik wrote:
>>>>>>Dirk Eddelbuettel writes:
>>>>>
> 
>>...
> 
> 
[...]
> 
> Best
> -k
> 
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
> 


-- 
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