[R-sig-Debian] R 2.7.2 kernlab issues

Dirk Eddelbuettel edd at debian.org
Thu Aug 28 04:34:31 CEST 2008


On 27 August 2008 at 13:24, Josh Stumpf wrote:
| Hello,
| After upgrading to 2.7.2 this morning via the cran repository, I get the
| following error when calling R via the command line:
| Error in dyn.load(file, DLLpath = DLLpath, ...) :
|   unable to load shared library
| '/home/jstumpf/R/i486-pc-linux-gnu-library/2.7/kernlab/libs/kernlab.so':
|   libRlapack.so: cannot open shared object file: No such file or directory
| Fatal error: unable to restore saved data in .RData

The libRlapack.so gives it away: You probably built / installed this with R
2.6.* or earlier when we had libRlapack. This changed with improved
Lapack/Blas/Atlas packages for Debian during the winter and the 2.7.* series
uses libblas.  

On my system (where I coincidentally just updated packages from CRAN a few
hours agao) I have

edd at ron:~> ldd /usr/local/lib/R/site-library/kernlab/libs/kernlab.so
        linux-gate.so.1 =>  (0xb7f21000)
        libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0xb7b5e000)
        libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0xb7aac000)
        liblapack.so.3gf => /usr/lib/atlas/liblapack.so.3gf (0xb7338000)
        libR.so => /usr/lib/R/lib/libR.so (0xb7044000)
        libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0xb6f57000)
        libm.so.6 => /lib/i686/cmov/libm.so.6 (0xb6f31000)
        libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb6f24000)
        libc.so.6 => /lib/i686/cmov/libc.so.6 (0xb6dc9000)
        libreadline.so.5 => /lib/libreadline.so.5 (0xb6d97000)
        libpcre.so.3 => /usr/lib/libpcre.so.3 (0xb6d6e000)
        libz.so.1 => /usr/lib/libz.so.1 (0xb6d59000)
        libdl.so.2 => /lib/i686/cmov/libdl.so.2 (0xb6d55000)
        /lib/ld-linux.so.2 (0xb7f22000)
        libncurses.so.5 => /lib/libncurses.so.5 (0xb6d23000)
edd at ron:~>     

which shows libblas and liblapack with the 3gf suffix indicating the new
Fortran builds I was referring to above.

The fix should be simple. Fire up R and run update.packages():

    $ R
    > update.packages()

and install the littler package and use update.r (my preference).

Hope this helps, Dirk

| Has anyone else had this issue? Any solutions?
| Joshua Stumpf
| Eastern Michigan University
| 	[[alternative HTML version deleted]]
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Three out of two people have difficulties with fractions.

More information about the R-SIG-Debian mailing list