Hi Everyone, I have a few fairly basic questions about upgrading and installing R packages. First off, I am using Ubuntu Hardy Heron and have R 2.7.1 installed and working perfectly. I usually access R via Emacs ESS interface which I am still trying to get the hang of. My questions and issues are as follows:
Question 1: I started R and wanted to upgrade the installed R packages. So, I issue the command >upgrade.packages() and after selecting the CRAN mirror sites, I get the following message: lattice : Version 0.17-8 installed in /usr/lib/R/library Version 0.17-10 available at http://www.ibiblio.org/pub/languages/R/CRAN Update (y/N/c)? (To this, I respond with "y", but then I get the following:) Warning in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : 'lib = "/usr/lib/R/library"' is not writable (Off course, it is NOT writable because it did not ask for the administrative password. Would you like to create a personal library '~/R/i486-pc-linux-gnu-library/2.7' to install packages into? (y/n) I do not want to create new directories; I just want to upgrade where the older version already exists. So I respond with "n" and get this:) Error in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : unable to install packages My question is how do I go about upgrading AND installing packages from within R by using administrative account? I must say that at least for now, I was able to get around this issue by staring R as: sudo R and then using upgrade.packages(). But I would like a better solution when I am already in an R session. Question 2: When I started R via sudo R and issued >upgrade.packages() I had problem upgrading lattice package. I got the following error message: * Installing *source* package 'lattice' ... ** libs gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c init.c -o init.o In file included from init.c:2: /usr/share/R/include/R.h:28:20: error: stdlib.h: No such file or directory /usr/share/R/include/R.h:29:19: error: stdio.h: No such file or directory In file included from /usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h:7, from /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:11, from /usr/share/R/include/R.h:30, from init.c:2: /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:122:61: error: limits.h: No such file or directory In file included from init.c:2: /usr/share/R/include/R.h:32:18: error: math.h: No such file or directory /usr/share/R/include/R.h:33:19: error: errno.h: No such file or directory In file included from /usr/share/R/include/R.h:50, from init.c:2: /usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or directory In file included from init.c:3: /usr/share/R/include/Rinternals.h:770: error: expected declaration specifiers or '...' before 'FILE' /usr/share/R/include/Rinternals.h:773: error: expected declaration specifiers or '...' before 'FILE' make: *** [init.o] Error 1 ERROR: compilation failed for package 'lattice' ** Removing '/usr/lib/R/library/lattice' ** Restoring previous '/usr/lib/R/library/lattice' The downloaded packages are in /tmp/Rtmpj37zYN/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package 'lattice' had non-zero exit status Even >upgrade.packages(dependencies = TRUE) resulted in the same error. Does anyone know if this is just a problem on my system or perhaps someone else has run into the same issue. What does this all mean? What I do not understand is why are there .h missing files? How the heck did lattice get installed in the first place if these header files were missing? Question 3: This is more of a general question that has been on my mind for sometime. If I just want to install some packages/data base etc that I would like to be "local", perhaps in my home directory, which library path would be recommended? Sometimes I feel that I would like to download some database or other packaged code that I want to play around with but would later like to get rid of, a library in the home directory that is still in R's path might be better. I would appreciate suggestions. What are others doing in this situation? Currently I have the following outcome of .libPaths() command: > .libPaths() [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library" [3] "/usr/lib/R/library" Which library path should I choose? Best regards, Tariq [[alternative HTML version deleted]] ______________________________________________ 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.
