[R] R/Ubuntu, “package ‘stats’ in options(”defaultPackages“) was not found”
Jeff Newmiller
jdnewmil at dcn.davis.CA.us
Wed Sep 17 16:39:51 CEST 2014
Try a different mirror? Precise is getting kind of old... they may not be keeping all of the old files on that mirror.
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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.
>>
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>> 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
>>
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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.
>>
>
>______________________________________________
>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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