[R] R/Ubuntu, “package ‘stats’ in options(”defaultPackages“) was not found”
davide.chicco at gmail.com
davide.chicco at gmail.com
Wed Sep 17 14:51:08 CEST 2014
Yes, I've followed the instructions described here:
http://cran.r-project.org/bin/linux/ubuntu/README
I've added
deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu precise/
to the /etc/apt/sources.list file.
Any idea?
Thanks a lot!
-- Davide
2014-09-17 2:42 GMT-04:00 Jeff Newmiller <jdnewmil at dcn.davis.ca.us>:
> Are you using the apt sources described on CRAN for Ubuntu? I don't expect stock 12.04 would give you R3.1.1, yet I have not seen this problem on machines using the CRAN apt repositories.
> ---------------------------------------------------------------------------
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> Sent from my phone. Please excuse my brevity.
>
> On September 16, 2014 6:40:31 PM PDT, "davide.chicco at gmail.com" <davide.chicco at gmail.com> wrote:
>>Sorry guys for the errors in my behavior. I apologize.
>>
>>I installed R by using commands:
>>apt-get install r-base
>>apt-get install r-base-dev
>>
>>Here's the output of sessioninfo();
>>
>>> sessionInfo()
>>R version 3.1.1 (2014-07-10)
>>Platform: i686-pc-linux-gnu (32-bit)
>>
>>locale:
>> [1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=it_IT.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=it_IT.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>>attached base packages:
>>[1] graphics grDevices utils datasets methods base
>>
>>loaded via a namespace (and not attached):
>>[1] tcltk_3.1.1 tools_3.1.1
>>
>>
>>Any idea? Thanks!
>>
>>-- Davide
>>
>>2014-09-16 17:15 GMT-04:00 David Winsemius <dwinsemius at comcast.net>:
>>>
>>> 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
>>>>
>>>>
>>>>
>>>> ______________________________________________
>>>> 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
>>>
>>
>>______________________________________________
>>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.
>
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