Hi Chris, Thanks for patient follow-up even after I (as Johannes noted) evidently overlooked key parts of your first email.
On 21 September 2011 at 07:49, Chris Evans wrote: | I ran synaptic from the Debian application menu which defaults to root | after askling for the root password the first time I invoke it after a | reboot. (I probably should have said that I've been using Debian for my | internet server work for about 15 years: I'm not a Debian/linux newbie, | just someone finally throwing away the reins from M$ to have a laptop | running Debian as well!) Perfect. | I get that from invoking update.packages() in an R session launched from | a user (chris) terminal session. Before that I had done an install of I do that too, as well as calling the 'install.r' helper script from littler (in its examples/ diretory, if interested). This requires that you make /usr/local/lib/R/site-library/ writable for _you_ as user chris, else you cannot. [ It also assumes that the Renviron setting mentioned last time is still valid, do this: edd@max:~$ R -q -e 'print(.libPaths())' R> print(.libPaths()) [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library" "/usr/lib/R/library" R> R> It _must_ be first as here. ] Now, /usr/local/lib/R/site-library/ comes shipped from the r-base-core package as owned by group 'staff' so one solution is to add yourself to group staff: edd@max:~$ ls -ld /usr/local/lib/R/site-library/ drwxrwsr-x 136 root staff 4096 2011-09-20 07:44 /usr/local/lib/R/site-library/ edd@max:~$ id uid=1000(edd) gid=1000(edd) groups=1000(edd),4(adm),20(dialout),24(cdrom),27(sudo),44(video),46(plugdev),50(staff),[.....] edd@max:~$ If those two conditions are met, you should be able to run install.packages() as you. I still prefer it from the shell as I sometimes need another apt-get call for a missing library etc. | I wouldn't dream of compiling locally anything I can get from a deb you | rolled!! :-) | However, I come back to feeling that there must be three separate | problems here that come from within the packages I added after the | initial r-cran-base install. My hunch is that there are things with XML | and rgl that I will be able to track down when restrict to just updating "I would not dream of compiling locally" either. You could start by locally re-building the packages. Which requires the build depends. | them but that at the moment there is a more global problem which I'm | guessing is caused by one package overriding the order of library path | options seen in .libPaths() which starts with a perfectly writable local | user directory and I am guessing there is some way that package has | insisted that the install tries /usr/lib/R/library. Agreed on the first bit. I think /usr/lib/R/library -- where we as users should never tread as it is /usr which belongs to apt/dpkg -- is just the fallback. Somehow the value got nuked. | I don't know enough about the way that R and linux work agree the use of | those library location options. From ?.libPaths and a bit more hunting | around the R help I had the impression that the .libPath options would | be used in order. I think I can remove the /usr ones by hacking in Correct. | /etc/R but that presumably risks losing access to the main libraries | that will have been installed there so that doesn't look a good step | forward except perhaps to debug things. An easier option ... is to _explicitly add_ the /usr/local/lib/R/site-library/ destination as an argument to install.packages! | I suspect that I could do a complete remove of all of R, start again | installing r-cran-base, check that R installed by that updates fine run | by a user and then I could use synaptic to add the additional deb | packages you provide but doing that one by one and running R and | update.packages() after each one to see if I don't hit this until afetr | a particular deb but that's going to take quite a long time so I | wondered if you or the list had quicker suggestions to debug this. That sounds too involved. | Sorry for length but hope that's clearer (got to try to be an acceptable | friend on R lists as well as with linux and I really, really do | appreciate the generosity of this list). No sweat. We're all just building karma :) Dirk -- New Rcpp master class for R and C++ integration is scheduled for San Francisco (Oct 8), more details / reg.info available at http://www.revolutionanalytics.com/products/training/public/rcpp-master-class.php _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
