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_
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
UPDATE: I have checked the lapack.so 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)
libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00186000)
...
checking the object
leonardo@LyP:~$ R CMD objdump -T /usr/lib/liblapack.so.3gf|grep dpstrf
00327f10 g DF .text 000024d4 Base dpstrf_
but
R CMD ldd /usr/lib/R/modules/lapack.so
linux-gate.so.1 => (0x009f5000)
libR.so => /usr/lib/R/lib/libR.so (0x00110000)
liblapack.so.3gf => /usr/lib/R/lib/liblapack.so.3gf (0x009f6000)
libblas.so.3gf => /usr/lib/R/lib/libblas.so.3gf (0x11eef000)
R links to another library and searching for the object:
leonardo@LyP:~$ R CMD objdump -T /usr/lib/R/lib/liblapack.so.3gf|grep dpstrf
gives empty
Any ideas?
I had the same problem and I tracked it to a conflict with the revolution-mkl package
sudo apt-get remove revolution-mkl
fixed the problem
I uninstall R using synaptics and marking all r-base and r-cran packages, reinstall it with
sudo apt-get install r-base r-base-dev r-base-html
and that's it, everything work fine.
Thanks to all the commenters!
Where did your mgcv package come from? CRAN as source? CRAN as a r-cran-mgcv via Michael's rebuild of my Debian package?
On my Ubuntu box, using the standard Ubuntu repo on CRAN, all is well:
edd@max:~$ ldd /usr/lib/R/library/mgcv/libs/mgcv.so
linux-vdso.so.1 => (0x00007ffff43ff000)
liblapack.so.3gf => /usr/lib/liblapack.so.3gf (0x00007f0374f75000)
libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00007f0373ad6000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f03737d9000)
libR.so => /usr/lib/libR.so (0x00007f0373215000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f0372e56000)
libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007f0372b3e000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f0372928000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f037270b000)
libreadline.so.6 => /lib/x86_64-linux-gnu/libreadline.so.6 (0x00007f03724c8000)
libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007f037228b000)
liblzma.so.5 => /usr/lib/x86_64-linux-gnu/liblzma.so.5 (0x00007f0372069000)
libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007f0371e58000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f0371c41000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f0371a39000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f0371834000)
libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f0371626000)
/lib64/ld-linux-x86-64.so.2 (0x00007f0375de2000)
libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f03713f0000)
libtinfo.so.5 => /lib/x86_64-linux-gnu/libtinfo.so.5 (0x00007f03711c8000)
edd@max:~$
and
edd@max:~$ 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: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
R> library(mgcv)
This is mgcv 1.7-22. For overview type 'help("mgcv-package")'.
R>
I had a similar problem, for me only starting R with sudo solved it.
