On Sep 18, 2014, at 10:28 AM, davide.chi...@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 <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.
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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.
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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.
David Winsemius, MD
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.
