[BioC] Errors with latest version of R/Bioconductor

[Claire Wilson]

Dear all,

I have just upgraded to R1.7.0/Bioconductor, with a little help from our local sys ad people.  However, when I start R I always get the following error:
>Creating a new generic function for "summary" in package
>reposTools
>
>Synching your local package management information ...
>
>        Note: reposTools can not access/usr/lbiosoft/lib/R/library.
>        This will not affect your R session unless you wish
>        to install/update/remove packages from this directory

I presume this is a permissions problem to do with accessing the directory, however the permissions are exactly the same as they are in R1.6.2/Bioconductor 1.1 and this runs fine

Furthermore, I have a .Rprofile file that runs the following commands
library(affy)
library(Biobase)
library(ctest)
library(annotate)
library(genefilter)
library(MASS)
library(tkWidgets)
library(mva)

Now in the latest version of R/Bioconductor, I get the following errors when I use my .Rprofile

>Welcome to Bioconductor
>         Vignettes contain introductory material.  To view,
>        simply type: openVignette()
>         For details on reading vignettes, see
>         the openVignette help page.
>Creating a new generic function for "summary" in package
>reposTools
>
>Synching your local package management information ...
>
>       Note: reposTools can not access/usr/lbiosoft/lib/R/library.
>        This will not affect your R session unless you wish
>        to install/update/remove packages from this directory
>
>Error in get(x, envir, mode, inherits) : variable "biplot" was not found
>Error in library(MASS) : package/namespace load failed

Yet when I remove my .Rprofile and load the libraries separately, I get no errors.

Any hints?

Thanks in advance

Claire
 
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