[BioC] writing of /usr/lib/R

[Liaw, Andy]

/usr/lib/R/library is the default place where packages are installed, but by
no means the only place where they can be installed.  Where R searches for
packages when asked is defined by the environment variable R_LIBS, which can
be defined in several possible places.  See the `Details' section of
?Startup (type that at the R prompt).

BTW, R-help is probably the more appropriate place for a non-BioC specific
question like this.  You're likely to get more useful help there.

Cheers,
Andy



> From: Michael Green
> 
> New to the list, first post!
> 
> I'm doing sysadmin work for our Bioinformatics department where I
> manage a couple of IBM BladeCenter based clusters. Systems are running
> SLES9 SP1 i586 (dual Xeon 32bit).
> Before I'm going to ask my question I must admit that I'm complete
> novice to R, and since I won't use it myself I didn't read much of the
> documentation supplied with the package. My question is more related
> to system administration + R, rather then to R itself.
> 
> So here it is:
> Some time ago I received a request from our users to install R on one
> of the clusters.
> I went ahead and installed R-base-2.1.0-1 supplied by the 
> vendor (SuSE/Novell).
> After that following the request of the users, I installed the
> Bioconductor packages using the standard procedure described at
> <http://www.bioconductor.org/download>:
> source("http://www.bioconductor.org/biocLite.R")
> biocLite()
> 
> Soon thereafter it became apparent that during their work with R, our
> users need to install/uninstall or otherwise change the hierarchy
> under /usr/lib/R  which is of course not writable by any user other
> than root. As you surely know that's the case for almost every
> directory under /usr. From talking to one of my users I've learned
> that R routinely downloads/installs/updates itself and the changes go
> into /usr/lib/R exclusively (or almost exclusively?).
> Now I'm faced with dilemma of how to allow users to write to
> /usr/lib/R, which is not a big deal on itself as there are at least a
> couple of ways doing that:
> 1. Play with standard unix permissions: create a new group for R
> users; chgrp <that_group> /usr/lib/R. etc...
> 2. Create ACL for /usr/lib/R
> 
> But my question is not about how to make /usrlib/R writable, but this:
> since /usr and everything under it is not traditionally writable by
> regular users what's the official stance of R developers on this? Is
> it assumed that all R users should have root access to the system
> where R installed to be able to change contents of /usr/lib/R and
> actually do any useful work?
> 
> About our R installation:
> bioinfo4:/usr/lib/R # R
> 
> R : Copyright 2005, The R Foundation for Statistical Computing
> Version 2.1.0  (2005-04-18), ISBN 3-900051-07-0
> 
> > sessionInfo()
> R version 2.1.0, 2005-04-18, i686-pc-linux-gnu
> 
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"   
>   "datasets"
> [7] "base"
> 
> --
> Warm regards,
> Michael Green
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
>