[BioC] Errors with latest version of R/Bioconductor

[Roger D. Peng]

As of 1.7.0, direct calls to library() should not be placed in 
.Rprofile.  Rather, you should use options("defaultPackages").  Try 
putting the following in your .Rprofile:

local({
   orig <- getOption("defaultPackages")
   options(defaultPackages = c(orig, 
"affy","Biobase","ctest","annotate","genefilter","MASS","tkWidgets","mva"))
 })

-roger

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
> 
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