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 at 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 at 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 at 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 at 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