Joris De Wolf
2005-Apr-29 13:54 UTC
[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(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}}
Peter Dalgaard
2005-Apr-29 14:16 UTC
[R] Error in La.chol2inv(x, size) : lapack routines cannot be loaded
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
Prof Brian Ripley
2005-Apr-29 14:20 UTC
[R] Error in La.chol2inv(x, size) : lapack routines cannot be loaded
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
Huntsinger, Reid
2005-Apr-29 14:26 UTC
[R] Error in La.chol2inv(x, size) : lapack routines cannot be loaded
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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