[R] R lapack routines cannot be loaded

Sat Nov 24 15:00:05 CET 2012

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-devel-discuss at 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 at 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 at 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 at LyP:~$

On Sat, Nov 24, 2012 at 5:05 AM, Prof Brian Ripley
<ripley at stats.ox.ac.uk> wrote:
> This was answered this week in
> https://stat.ethz.ch/pipermail/r-help/2012-November/329946.html
>
>
> On 23/11/2012 16:05, 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
>>
>> 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-help at 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.
>>
>
>
> --
> 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