[R] R lapack routines cannot be loaded

[arysar]

I usually ran different statistical analysis in R with routines that
use lapack like gam() lm(), etc but after several updates of libraries
the following error appears:

library(mgcv)
This is mgcv 1.7-22. For overview type 'help("mgcv-package")'.

model <- with(chlaR,gam(ClorMAX ~ s(DegDay_NM)))
Error en eigen(St, symmetric = TRUE) :
lapack routines cannot be loaded
Además: Mensajes de aviso perdidos
In eigen(St, symmetric = TRUE) :
unable to load shared object '/usr/lib/R/modules//lapack.so':
/usr/lib/R/modules//lapack.so: undefined symbol: dpstrf_

model <- with(chlaR,lm(ClorMAX ~ DegDay_NM))
summary(model)
Error en chol2inv(Qr$qr[p1, p1, drop = FALSE]) :
lapack routines cannot be loaded

The version information is:

platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major 2
minor 15.2
year 2012
month 10
day 26
svn rev 61015
language R

I am using Ubuntu 12.04.1 LTS

Any ideas?

______________________________________________
R-h...@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Martin Morgan]

On 11/23/2012 08:05 AM, arysar wrote:
> I usually ran different statistical analysis in R with routines that
> use lapack like gam() lm(), etc but after several updates of libraries
> the following error appears:
>
> library(mgcv)
> This is mgcv 1.7-22. For overview type 'help("mgcv-package")'.
>
> model <- with(chlaR,gam(ClorMAX ~ s(DegDay_NM)))
> Error en eigen(St, symmetric = TRUE) :
> lapack routines cannot be loaded
> Además: Mensajes de aviso perdidos
> In eigen(St, symmetric = TRUE) :
> unable to load shared object '/usr/lib/R/modules//lapack.so':
> /usr/lib/R/modules//lapack.so: undefined symbol: dpstrf_
>
> model <- with(chlaR,lm(ClorMAX ~ DegDay_NM))
> summary(model)
> Error en chol2inv(Qr$qr[p1, p1, drop = FALSE]) :
> lapack routines cannot be loaded
>

https://stat.ethz.ch/pipermail/r-help/2012-November/329946.html

> The version information is:
>
> platform i686-pc-linux-gnu
> arch i686
> os linux-gnu
> system i686, linux-gnu
> status
> major 2
> minor 15.2
> year 2012
> month 10
> day 26
> svn rev 61015
> language R
>
> I am using Ubuntu 12.04.1 LTS
>
> Any ideas?
>
> ______________________________________________
> R-h...@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

[Prof Brian Ripley]

This was answered this week in
https://stat.ethz.ch/pipermail/r-help/2012-November/329946.html

--
Brian D. Ripley, rip...@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

[arysar]

Yes I read that link but I have lapack version 3.3.1-1:


Paquete: liblapack3gf
Nuevo: sí
Estado: instalado
Instalado automáticamente: sí
Versión: 3.3.1-1
Prioridad: opcional
Sección: libs
Desarrollador: Ubuntu Developers <ubuntu-dev...@lists.ubuntu.com>
Arquitectura: i386
Tamaño sin comprimir: 8.098 k
Depende de: debconf (>= 0.5) | debconf-2.0, libblas3gf |
libblas.so.3gf | libatlas3gf-base, libc6 (>=
2.1.3), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6)
Tiene conflictos con: lapack99
Reemplaza: lapack99
Proporciona: liblapack.so.3gf


just to confirm the problem:

leonardo@LyP:~$ R

R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i686-pc-linux-gnu (32-bit)

R es un software libre y viene sin GARANTIA ALGUNA.
Usted puede redistribuirlo bajo ciertas circunstancias.
Escriba 'license()' o 'licence()' para detalles de distribucion.

R es un proyecto colaborativo con muchos contribuyentes.
Escriba 'contributors()' para obtener más información y
'citation()' para saber cómo citar R o paquetes de R en publicaciones.

Escriba 'demo()' para demostraciones, 'help()' para el sistema on-line de ayuda,
o 'help.start()' para abrir el sistema de ayuda HTML con su navegador.
Escriba 'q()' para salir de R.

> example(chol)

chol> ( m <- matrix(c(5,1,1,3),2,2) )
[,1] [,2]
[1,] 5 1
[2,] 1 3

chol> ( cm <- chol(m) )
Error en chol.default(m) : rutinas lapack no pueden ser cargadas

Además: Mensajes de aviso perdidos

In chol.default(m) :

unable to load shared object '/usr/lib/R/modules//lapack.so':
/usr/lib/R/modules//lapack.so: undefined symbol: dpstrf_

but the object lapack.so exist and is properly linked to
liblapack.so.3gf library


leonardo@LyP:~$ ldd /usr/lib/R/modules/lapack.so
linux-gate.so.1 => (0x009ec000)
libR.so => /usr/lib/libR.so (0x0023a000)
liblapack.so.3gf => /usr/lib/liblapack.so.3gf (0x00ba3000)
libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0x00622000)
libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0x0064e000)
libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00186000)
libreadline.so.6 => /lib/i386-linux-gnu/libreadline.so.6 (0x00110000)
libpcre.so.3 => /lib/i386-linux-gnu/libpcre.so.3 (0x0014a000)
liblzma.so.5 => /usr/lib/i386-linux-gnu/liblzma.so.5 (0x00203000)
libbz2.so.1.0 => /lib/i386-linux-gnu/libbz2.so.1.0 (0x008d0000)
libz.so.1 => /lib/i386-linux-gnu/libz.so.1 (0x005d4000)
librt.so.1 => /lib/i386-linux-gnu/librt.so.1 (0x0022a000)
libdl.so.2 => /lib/i386-linux-gnu/libdl.so.2 (0x00233000)
libgomp.so.1 => /usr/lib/i386-linux-gnu/libgomp.so.1 (0x00a17000)
libpthread.so.0 => /lib/i386-linux-gnu/libpthread.so.0 (0x005ea000)
/lib/ld-linux.so.2 (0x00b4f000)
libgfortran.so.3 => /usr/lib/i386-linux-gnu/libgfortran.so.3 (0x008e1000)
libgcc_s.so.1 => /lib/i386-linux-gnu/libgcc_s.so.1 (0x007f8000)
libtinfo.so.5 => /lib/i386-linux-gnu/libtinfo.so.5 (0x00816000)
libquadmath.so.0 => /usr/lib/i386-linux-gnu/libquadmath.so.0 (0x00835000)



leonardo@LyP:~$