[Fwd: Re: ubuntu problem with 'r-cran-robustbase' [FWD Agustin Lobo]]
Good (but astonishing) news: 1. (As noted in previous message) After having removed r-base-core and installed back r-base and r-base-dev the binary installation of robustbase apt-get install r-cran-robustbase still gives in R the same error as before:
require(robustbase)
Loading required package: robustbase
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/usr/lib/R/site-library/robustbase/libs/robustbase.so':
libRlapack.so: cannot open shared object file: No such file or directory
2. After removing the binary
apt-get remove r-cran-robustbase
The source installation using install.packages("robustbase") from within
R works fine. The gcc step now works using lapack:
gcc -std=gnu99 -shared -o robustbase.so R-rng4ftn.o init.o lmrob.o mc.o
qn_sn.o rf-common.o rffastmcd.o rfltsreg.o wgt_himed.o -llapack -lblas
-lgfortran -lm -lgfortran -lm -L/usr/lib/R/lib -lR
Thank you all.
Agus
Michael Rutter wrote:
Once you have reinstalled the packages, you should re-install robustbase.
sudo R
install.packages("robustbase")
If at that point it fails, I'm not sure what can be done. It would seem
you system has a flaw and a re-install would be best. Jaunty (9.04)
installs very quickly and works great. I would give that a try.
Michael
Agustin Lobo wrote:
No. What I have is what is listed in http://cran.r-project.org/bin/linux/ubuntu/ deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu hardy/ which in my case is deb http://cran.r-project.org/bin/linux/ubuntu hardy/ Should I include the one you suggest? Should I replace the one I have with this one? Agus Michael Rutter wrote:
Agus, Do you have this in your sources list: deb http://lib.stat.cmu.edu/R/CRAN/bin/linux/ubuntu hardy/ The address could/should be a different mirror, but there needs to be a cran mirror in you list somewhere. Michael Agustin Lobo wrote:
Michael: I do have the backports activated. This is the entry in my sources.list: deb http://archive.ubuntu.com/ubuntu/ hardy-backports restricted main multiverse universe deb-src http://archive.ubuntu.com/ubuntu/ hardy-backports restricted main multiverse universe And this is the output to what you suggested. root at alobo-laptop:/home/alobo# dpkg --get-selections | grep r-base r-base-core install r-base-dev install r-base-html install root at alobo-laptop:/home/alobo# dpkg --get-selections | grep r-cran r-cran-abind deinstall r-cran-boot install r-cran-cluster install r-cran-codetools install r-cran-effects deinstall r-cran-foreign install r-cran-kernsmooth install r-cran-lattice install r-cran-matrix install r-cran-mgcv install r-cran-nlme install r-cran-relimp deinstall r-cran-robustbase install r-cran-rpart install r-cran-survival install r-cran-vr install My system is uptodate, I regularly install what I'm told by Update Manager. I'm going to uninstall and install back r-base from Synaptic. If I keep having the same problem afterwards, do you expect that installing everything from sources could solve the problem? Will it be hard ? How much time should I pre-allocate? Thanks Agus Michael Rutter wrote:
Agus, robustbase just installed fine on my stock 8.04 system. Please make sure that you have added all the repositories and packages suggested on this page: http://cran.r-project.org/bin/linux/ubuntu/ Backports are important, and make sure you have r-base-dev installed. You may also need to be root (via sudo) to install, although there are instructions for local installation. You can run the following commands to see what R related packages you have installed. dpkg --get-selections | grep r-base dpkg --get-selections | grep r-cran Michael