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

David Winsemius dwinsemius at comcast.net
Fri Sep 19 07:02:12 CEST 2014 

On Sep 18, 2014, at 10:28 AM, davide.chicco at gmail.com wrote:

> I tried with a different mirror, but nothing changed...
>
> Any other idea?

Post to the r-SIG--debian mailing list?
Search that list's Archives?

--  
David.
>
> Thanks anyway
>
> -- Davide
>
> 2014-09-17 10:39 GMT-04:00 Jeff Newmiller <jdnewmil at dcn.davis.ca.us>:
>> Try a different mirror? Precise is getting kind of old... they may  
>> not be keeping all of the old files on that mirror.
>>
>> ---------------------------------------------------------------------------
>> Jeff Newmiller                        The     .....       .....  Go  
>> Live...
>> DCN:<jdnewmil at dcn.davis.ca.us>        Basics: ##.#.       ##.#.   
>> Live Go...
>>                                      Live:   OO#.. Dead: OO#..   
>> Playing
>> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
>> /Software/Embedded Controllers)               .OO#.       .OO#.   
>> rocks...1k
>> ---------------------------------------------------------------------------
>> Sent from my phone. Please excuse my brevity.
>>
>> On September 17, 2014 5:51:08 AM PDT, "davide.chicco at gmail.com" <davide.chicco at gmail.com 
>> > wrote:
>>> 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.
>>>>
>>> ---------------------------------------------------------------------------
>>>> Jeff Newmiller                        The     .....       .....  Go
>>> Live...
>>>> DCN:<jdnewmil at dcn.davis.ca.us>        Basics: ##.#.       ##.#.   
>>>> Live
>>> Go...
>>>>                                      Live:   OO#.. Dead: OO#..
>>> Playing
>>>> Research Engineer (Solar/Batteries            O.O#.       #.O#.   
>>>> with
>>>> /Software/Embedded Controllers)               .OO#.       .OO#.
>>> rocks...1k
>>>>
>>> ---------------------------------------------------------------------------
>>>> 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.
>>>>
>>>
>>> ______________________________________________
>>> 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.
>>
>
>
>
> -- 
>
>
> ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
>  Davide Chicco
> Postdoctoral Fellow
> Michael M. Hoffman Lab
> 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, MD
Alameda, CA, USA

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