R help - Apr 2005 - Error in La.chol2inv(x, size) : lapack routines cannot be loaded

Dear all,

OS: x86_64-suse-linux 9.2
CPU: Intel(R) Xeon(TM) CPU 3.20GHz
R-version: R-2.1.0

I've started using a new Linux server, upgraded at the same time to 
R-2.1.0 (see above) and have problems with some elementary analysis that 
ran without a problem on my previous configuration.

anova.glm gives the following error:

Error in La.chol2inv(x, size) : lapack routines cannot be loaded

This was with the after the following configure

./configure --with-readline --prefix=/opt/R-2.1.0 --with-libpng 
--with-jpeglib --with-pcre --without-x

The obvious thing to try next was:

./configure --with-readline --prefix=/opt/R-2.1.0 --with-libpng 
--with-jpeglib --with-pcre --without-x --with-lapack

but this gave errors at the make:

make[3]: Entering directory `/usr/local/src/R-2.1.0/src/modules/lapack'
make[4]: Entering directory `/usr/local/src/R-2.1.0/src/modules/lapack'
make[4]: `Makedeps' is up to date.
make[4]: Leaving directory `/usr/local/src/R-2.1.0/src/modules/lapack'
make[4]: Entering directory `/usr/local/src/R-2.1.0/src/modules/lapack'
gcc -shared -L/usr/local/lib -o lapack.so  Lapack.lo   -llapack -lblas 
-lg2c -lm -lgcc_s
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../x86_64-suse-linux/bin/ld:
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../lib64/liblapack.a(dgecon.i):
relocation R_X86_64_32 against `a local symbol' can not be used when 
making a shared object; recompile with -fPIC
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../lib64/liblapack.a: 
could not read symbols: Bad value
collect2: ld returned 1 exit status
make[4]: *** [lapack.so] Error 1

I've found some similar postings  about Debian, but without a soluition.

Any idea how I could proceed?

Joris










confidentiality notice:
The information contained in this e-mail is confidential and...{{dropped}}

Joris De Wolf <joris.dewolf at cropdesign.com> writes:
> Dear all,
> 
> OS: x86_64-suse-linux 9.2
> CPU: Intel(R) Xeon(TM) CPU 3.20GHz
> R-version: R-2.1.0
> 
> I've started using a new Linux server, upgraded at the same time to
> R-2.1.0 (see above) and have problems with some elementary analysis
> that ran without a problem on my previous configuration.
> 
> anova.glm gives the following error:
> 
> Error in La.chol2inv(x, size) : lapack routines cannot be loaded
> 
> This was with the after the following configure
> 
> ./configure --with-readline --prefix=/opt/R-2.1.0 --with-libpng
> --with-jpeglib --with-pcre --without-x
> 
> The obvious thing to try next was:
> 
> ./configure --with-readline --prefix=/opt/R-2.1.0 --with-libpng
> --with-jpeglib --with-pcre --without-x --with-lapack
> 
> but this gave errors at the make:
> 
> make[3]: Entering directory `/usr/local/src/R-2.1.0/src/modules/lapack'
> make[4]: Entering directory `/usr/local/src/R-2.1.0/src/modules/lapack'
> make[4]: `Makedeps' is up to date.
> make[4]: Leaving directory `/usr/local/src/R-2.1.0/src/modules/lapack'
> make[4]: Entering directory `/usr/local/src/R-2.1.0/src/modules/lapack'
> gcc -shared -L/usr/local/lib -o lapack.so  Lapack.lo   -llapack -lblas
> -lg2c -lm -lgcc_s
>
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../x86_64-suse-linux/bin/ld:
>
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../lib64/liblapack.a(dgecon.i):
> relocation R_X86_64_32 against `a local symbol' can not be used when
> making a shared object; recompile with -fPIC
> /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../lib64/liblapack.a:
> could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make[4]: *** [lapack.so] Error 1
> 
> I've found some similar postings  about Debian, but without a
soluition.
> 
> Any idea how I could proceed?
Which compilers are you using? What is the output from configure?

Unless something drastic happened between 9.1 and 9.2, you should be
able to just ./configure without further decorations (except possibly
--without-x if you can't be bothered to install the xorg-x11-devel
RPM).

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907

Your subject line is misleading: you ignored a warning during make.

The solution is not to specify all the confgure flags you can think of, 
and allow R to choose.  Only once you have it working with the defaults 
try substituting other libraries.

Your particular problem is that you have a non-shareable liblapack in your 
library path.  Do see the warnings about this on 64-bit systems in the
R-admin manual (you know, the one the INSTALL file asks you to read if 
you run into problems!).

On Fri, 29 Apr 2005, Joris De Wolf wrote:
> Dear all,
>
> OS: x86_64-suse-linux 9.2
> CPU: Intel(R) Xeon(TM) CPU 3.20GHz
> R-version: R-2.1.0
>
> I've started using a new Linux server, upgraded at the same time to
R-2.1.0
> (see above) and have problems with some elementary analysis that ran
without
> a problem on my previous configuration.
>
> anova.glm gives the following error:
>
> Error in La.chol2inv(x, size) : lapack routines cannot be loaded
>
> This was with the after the following configure
>
> ./configure --with-readline --prefix=/opt/R-2.1.0 --with-libpng 
> --with-jpeglib --with-pcre --without-x
>
> The obvious thing to try next was:
>
> ./configure --with-readline --prefix=/opt/R-2.1.0 --with-libpng 
> --with-jpeglib --with-pcre --without-x --with-lapack
>
> but this gave errors at the make:
>
> make[3]: Entering directory `/usr/local/src/R-2.1.0/src/modules/lapack'
> make[4]: Entering directory `/usr/local/src/R-2.1.0/src/modules/lapack'
> make[4]: `Makedeps' is up to date.
> make[4]: Leaving directory `/usr/local/src/R-2.1.0/src/modules/lapack'
> make[4]: Entering directory `/usr/local/src/R-2.1.0/src/modules/lapack'
> gcc -shared -L/usr/local/lib -o lapack.so  Lapack.lo   -llapack -lblas
-lg2c
> -lm -lgcc_s
>
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../x86_64-suse-linux/bin/ld:
>
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../lib64/liblapack.a(dgecon.i):
> relocation R_X86_64_32 against `a local symbol' can not be used when
making a
> shared object; recompile with -fPIC
> /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../lib64/liblapack.a: 
> could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make[4]: *** [lapack.so] Error 1
>
> I've found some similar postings  about Debian, but without a
soluition.
I am unaware of any unresolved issues of this type that are not covered in 
the installation manual.
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

Your Linux distribution has a static Lapack library that you can't use for R
because it wasn't compiled into "position-independent" code.
That's a
standard Lapack build, but won't work to make a dynamically loadable
library. That's why the second attempt doesn't build.

I'm not sure I can help further without knowing a little more. The first
thing I would do, though, is to try a plain build without install and see
what's happening. If it's the same behavior, you might try checking how
R
(the script that starts the executable) sets up the environment,
particularly LD_LIBRARY_PATH. Does lapack.so get built? How? Do you have a
BLAS on your system, or does it use R's? The output of configure would help
to see what's being picked up. (I don't have a 64 bit machine handy so I
can't go out and try any of these right now...)

Reid Huntsinger


-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Joris De Wolf
Sent: Friday, April 29, 2005 9:54 AM
To: r-help at stat.math.ethz.ch
Subject: [R] Error in La.chol2inv(x, size) : lapack routines cannot be
loaded


Dear all,

OS: x86_64-suse-linux 9.2
CPU: Intel(R) Xeon(TM) CPU 3.20GHz
R-version: R-2.1.0

I've started using a new Linux server, upgraded at the same time to 
R-2.1.0 (see above) and have problems with some elementary analysis that 
ran without a problem on my previous configuration.

anova.glm gives the following error:

Error in La.chol2inv(x, size) : lapack routines cannot be loaded

This was with the after the following configure

./configure --with-readline --prefix=/opt/R-2.1.0 --with-libpng 
--with-jpeglib --with-pcre --without-x

The obvious thing to try next was:

./configure --with-readline --prefix=/opt/R-2.1.0 --with-libpng 
--with-jpeglib --with-pcre --without-x --with-lapack

but this gave errors at the make:

make[3]: Entering directory `/usr/local/src/R-2.1.0/src/modules/lapack'
make[4]: Entering directory `/usr/local/src/R-2.1.0/src/modules/lapack'
make[4]: `Makedeps' is up to date.
make[4]: Leaving directory `/usr/local/src/R-2.1.0/src/modules/lapack'
make[4]: Entering directory `/usr/local/src/R-2.1.0/src/modules/lapack'
gcc -shared -L/usr/local/lib -o lapack.so  Lapack.lo   -llapack -lblas 
-lg2c -lm -lgcc_s
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../x86_64-suse-linux/bin
/ld: 
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../lib64/liblapack.a(dge
con.i): 
relocation R_X86_64_32 against `a local symbol' can not be used when 
making a shared object; recompile with -fPIC
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../lib64/liblapack.a: 
could not read symbols: Bad value
collect2: ld returned 1 exit status
make[4]: *** [lapack.so] Error 1

I've found some similar postings  about Debian, but without a soluition.

Any idea how I could proceed?

Joris










confidentiality notice:
The information contained in this e-mail is confidential and...{{dropped}}

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