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

[Huntsinger, Reid]

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










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