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

Jeff Newmiller jdnewmil at dcn.davis.CA.us
Wed Sep 17 08:42:28 CEST 2014 

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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