[R] R/Ubuntu, “package ‘stats’ in options(”defaultPackages“) was not found”
davide.chicco at gmail.com
davide.chicco at gmail.com
Thu Sep 18 16:28:42 CEST 2014
I tried with a different mirror, but nothing changed...
Any other idea?
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...
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> 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
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