And as a followup: what I do in a multi-user environment (and after some
years of experience I think this is the best approach) is to immediately
make a site-library directory where I install all packages.  Basically we
have groups like
  1) me
  2) people allowed to install R packages system-wide
  3) most users
I set the permissions of site-library to be 2), but the standard library is
always 1) because it is installed as part of R.  This mean any user in 2)
who (say) tried to update all installed R packages system-wide will be told
that the packages included with R cannot be updated; exactly the situation
the OP described.

Best,
Kasper




On Sun, Jun 1, 2014 at 8:19 AM, Wolfgang Huber <whuber@embl.de> wrote:

>
> On 31 May 2014, at 23:53, Steve Lianoglou <lianoglou.steve@gene.com>
> wrote:
> > On Sat, May 31, 2014 at 1:46 PM, Felix Francis [guest]
> >> While trying to install Bioconductor, I get this warning message:
> >> installed directory not writable, cannot update packages 'boot',
> 'class', 'cluster', 'foreign', 'KernSmooth', 'lattice', 'MASS',
> >>  'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial'
> >
> > It sounds like you do not have permissions to write into the installed
> > directory that R was installed in on the computer you are using.
> >
> > Running the update/install as an administrator on the machine would
> > likely do the trick.
>
> Depending on how valuable the machine is, or how many users work with it,
> it is preferable to install R as well as its libraries with an account with
> limited rights; and then to use that account also for package updates and
> the installation of additional packages, as what Felix is trying to do.
>
> Doing it as administrator seems like leaving a hole for through which bad
> things could be done (intentionally or unintentionally) . I’ve not yet seen
> this actually happening, though.
>
>         Wolfgang
>
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