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 <jdnew...@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:<jdnew...@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.chi...@gmail.com" > <davide.chi...@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 <jdnew...@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:<jdnew...@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.chi...@gmail.com" >><davide.chi...@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 <dwinsem...@comcast.net>: >>>>> >>>>> On Sep 16, 2014, at 12:19 PM, davide.chi...@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@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@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@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.chi...@gmail.com web: http://www.DavideChicco.it :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: ______________________________________________ R-help@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.
