Upgrading to R 2.15.2 can't load stats package

Question

Running Ubuntu 12.04. finally upgraded from 2.12 to 2.15.2 today and when I start R I get this error.

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/usr/lib/R/library/stats/libs/stats.so':
  /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chemv
During startup - Warning message:
package ‘stats’ in options("defaultPackages") was not found

edit:

$ dpkg -l | grep "blas\|atlas"
ii  libatlas3gf-base                               3.8.4-3build1                                 Automatically Tuned Linear Algebra Software, generic shared
ii  libblas-dev                                    1.2.20110419-2ubuntu1                         Basic Linear Algebra Subroutines 3, static library
ii  libblas3gf                                     1.2.20110419-2ubuntu1                         Basic Linear Algebra Reference implementations, shared library
ii  libopenblas-base                               0.1alpha2.2-3                                 Optimized BLAS (linear algebra) library based on GotoBLAS2
ii  libopenblas-dev                                0.1alpha2.2-3                                 Optimized BLAS (linear algebra) library based on GotoBLAS2

Anyone else have this problem or know how to fix?

added the deb http:///bin/linux/ubuntu precise/ repository. then just sudo apt-get update. sudo apt-get upgrade — sayhey69, Dec 07 '12 at 18:50
Please add to your question the output of `dpkg -l | grep "blas\|atlas"` — GSee, Dec 07 '12 at 19:05
Related: http://stackoverflow.com/questions/8917977/installing-lapack-for-numpy — GSee, Dec 07 '12 at 19:25

score 9 · Accepted Answer · answered Dec 07 '12 at 19:07

9

You should uninstall libopenblas-base

See this for more: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=638236

On my box:

$ dpkg -l | grep "blas\|atlas"
ii  libatlas-dev                                   3.8.4-3build1                           Automatically Tuned Linear Algebra Software, C header files
ii  libatlas3gf-base                               3.8.4-3build1                           Automatically Tuned Linear Algebra Software, generic shared
ii  libblas-dev                                    1.2.20110419-2ubuntu1                   Basic Linear Algebra Subroutines 3, static library
ii  libblas3gf                                     1.2.20110419-2ubuntu1                   Basic Linear Algebra Reference implementations, shared library
ii  liblastfm0                                     0.4.0~really0.3.3-0ubuntu1              The Last.fm web services library

answered Dec 07 '12 at 19:07

GSee

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Is there a way for the CRAN/debian maintainers to manage this conflict in the package process? – Ben Bolker Dec 07 '12 at 19:09
1

Thanks. Is this a common issue? – sayhey69 Dec 07 '12 at 19:13
@sayhey69, I don't know if it's common. I ran into a similar problem when I had revolution-mkl installed, so I knew where to look.. – GSee Dec 07 '12 at 19:20
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Can we get more upvotes for this answer! If only i had seen this before would have saved me some sleepless nights!! – ajkl May 05 '15 at 10:35

Upgrading to R 2.15.2 can't load stats package

1 Answers1

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