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

3 messages · Joris De Wolf, Peter Dalgaard, Brian Ripley

Joris De Wolf
# 
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










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Peter Dalgaard
# 
Joris De Wolf <joris.dewolf at cropdesign.com> writes:
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).
Brian Ripley
# 
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:

            

      
      
      
    

        
I am unaware of any unresolved issues of this type that are not covered in 
the installation manual.