[BioC] Errors with latest version of R/Bioconductor

[Robert Gentleman]

Hi Claire,
  You really need R 1.7.0 (patched), available at:
http://www.stats.uwo.ca/faculty/murdoch/software/r-devel/

  there are some bugs in R 1.7.0 that make it incompatible with much
  of the bioconductor software.

 Robert

On Tue, Jun 03, 2003 at 05:50:56PM +0100, Claire Wilson wrote:
> 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
>  
> --------------------------------------------------------
> 
>  
> This email is confidential and intended solely for the use of th... {{dropped}}
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

-- 
+---------------------------------------------------------------------------+
| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
| Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |
+---------------------------------------------------------------------------+