davide.chicco at gmail.com
2014-Sep-16 19:19 UTC
[R] R/Ubuntu, “package ‘stats’ in options(”defaultPackages“) was not found”
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
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
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
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
David Winsemius
2014-Sep-16 21:15 UTC
[R] R/Ubuntu, “package ‘stats’ in options(”defaultPackages“) was not found”
On Sep 16, 2014, at 12:19 PM, davide.chicco at gmail.com wrote:> 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(You were asked in the Posting Guide to not crosspost. And when you post to Stack Overflow you should respond to requests for clarification which you have not done either. You will never get useful answers if you don't respond to requests for clarification.)> > I have just installed R 3.1.1 on my Linux Ubuntu 12.04.5 LTS.More details are needed. How did you do this?> Then Iwanted 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.That would be somewhat unusual, but possible. You were asked in the Rhelp Posting Guide to provide the output of sessionInfo(). -- David. ]> 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 > > > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > 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 > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > > ______________________________________________ > 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.David Winsemius Alameda, CA, USA