[BioC] Bioconductor and R_LIBS

[Seth Falcon]

Hi Steve,

Steve Taylor <stephen.taylor at molecular-sciences.ox.ac.uk> writes:
> I had read that it is possible to point to a personal library
> directory by setting the environment variable R_LIBS. Even when I do
> this, when loading a library it still appears to be trying to write to
> the system R/2.0.1/lib/R/library/liblisting.Rda.
>
> For example:
>
>  > .libPaths()
> [1] "/home/cbrg/validate/myRlibs"    "/package/R/2.0.1/lib/R/library"
>  > library(affy)
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
>           Vignettes contain introductory material.  To view,
>           simply type: openVignette()
>           For details on reading vignettes, see
>           the openVignette help page.
> Loading required package: reposTools
> Warning messages:
> 1: Incorrect permissions to edit package database,
> /package/R/2.0.1/lib/R/library/liblisting.Rda in:
> save.locLib(locLibList, curLib)
> 2: Incorrect permissions to edit package database,
> /package/R/2.0.1/lib/R/library/liblisting.Rda in:
> save.locLib(locLibList, curLib)

Can you post the output of sessionInfo() after reproducing the session
as above?  

> In this case, this doesn't stop the user using the affy package (in
> fact this seems to be an issue with reposTools) but the warnings are
> a little disconcerting.

Yes, this is not desired/intended behavior and we'll see what we can
do to resolve it.

Note that setting R_LIBS has an effect on where packages will be
installed (after setting it) and the search path for packages.  Since
all the relevant packages are in the system-level package lib, setting
R_LIBS does not make any difference in your case (and that is as
expected).

Best,

+ seth