[R] R/Ubuntu, “package ‘stats’ in options(”defaultPackages“) was not found”

[davide.chicco at gmail.com]

Hi guys
I'm having some troubles in installing the "topicmodels" package in my
R system on a Linux Ubuntu machine.
I also described the problem here: http://bit.ly/1m8Ah6Z

I have just installed R 3.1.1 on my Linux Ubuntu 12.04.5 LTS. Then I
wanted to install the topicmodels package, and so I type
install.packages("topicmodels"), but the installation did not work.

It seems that I do not have the "stats" package installed in my
default packages. Here's the log:

++++++LOG+START++++++++++++++++++++

> install.packages("topicmodels");
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
also installing the dependencies ‘modeltools’, ‘slam’, ‘tm’

provo con l'URL
'http://cran.utstat.utoronto.ca/src/contrib/modeltools_0.2-21.tar.gz'
Content type 'application/x-gzip' length 14794 bytes (14 Kb)
URL aperto
==================================================
downloaded 14 Kb

provo con l'URL 'http://cran.utstat.utoronto.ca/src/contrib/slam_0.1-32.tar.gz'
Content type 'application/x-gzip' length 46672 bytes (45 Kb)
URL aperto
==================================================
downloaded 45 Kb

provo con l'URL 'http://cran.utstat.utoronto.ca/src/contrib/tm_0.6.tar.gz'
Content type 'application/x-gzip' length 505212 bytes (493 Kb)
URL aperto
==================================================
downloaded 493 Kb

provo con l'URL
'http://cran.utstat.utoronto.ca/src/contrib/topicmodels_0.2-1.tar.gz'
Content type 'application/x-gzip' length 847889 bytes (828 Kb)
URL aperto
==================================================
downloaded 828 Kb

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
Durante l'avvio - Warning message:
package ‘stats’ in options("defaultPackages") was not found
* installing *source* package ‘modeltools’ ...
** package ‘modeltools’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
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
Error : package ‘stats’ could not be loaded
ERROR: lazy loading failed for package ‘modeltools’
* removing ‘/usr/local/lib/R/site-library/modeltools’
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
Durante l'avvio - Warning message:
package ‘stats’ in options("defaultPackages") was not found
* installing *source* package ‘slam’ ...
** package ‘slam’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2
-fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security
-Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c apply.c -o apply.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2
-fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security
-Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c grouped.c -o
grouped.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2
-fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security
-Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c sparse.c -o
sparse.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2
-fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security
-Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c util.c -o util.o
gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o
slam.so apply.o grouped.o sparse.o util.o -lblas -lgfortran -lm
-lquadmath -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/slam/libs
** R
** preparing package for lazy loading
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
ERROR: lazy loading failed for package ‘slam’
* removing ‘/usr/local/lib/R/site-library/slam’
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
Durante l'avvio - Warning message:
package ‘stats’ in options("defaultPackages") was not found
ERROR: dependency ‘slam’ is not available for package ‘tm’
* removing ‘/usr/local/lib/R/site-library/tm’
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
Durante l'avvio - Warning message:
package ‘stats’ in options("defaultPackages") was not found
ERROR: dependencies ‘modeltools’, ‘slam’, ‘tm’ are not available for
package ‘topicmodels’
* removing ‘/usr/local/lib/R/site-library/topicmodels’

The downloaded source packages are in
    ‘/tmp/RtmpIppG4O/downloaded_packages’
Warning messages:
1: In install.packages("topicmodels") :
  installation of package ‘modeltools’ had non-zero exit status
2: In install.packages("topicmodels") :
  installation of package ‘slam’ had non-zero exit status
3: In install.packages("topicmodels") :
  installation of package ‘tm’ had non-zero exit status
4: In install.packages("topicmodels") :
  installation of package ‘topicmodels’ had non-zero exit status

++++++LOG+END++++++++++++++++++++

Here's the output of the dpkg -l | grep "blas\|atlas" command:

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

Do you have any idea on how to solve this problem?

Thanks a lot!

-- Davide


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  Davide Chicco
Postdoctoral Fellow
Princess Margaret Cancer Centre, University of Toronto
Toronto Medical Discovery Tower 11-401
101 College St, Toronto, Ontario M5G 1L7, Canada
mail: davide.chicco at gmail.com
web: http://www.davidechicco.it
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