[BioC] Failure to load Biobase

[Jenny Drnevich]

Hi all,

I'm having some trouble loading Biobase properly upon start up using 
.Rprofile in a Windows environment. I saw this problem before, but I 
mistakenly attributed it to a problem in the affy package affecting hist() 
in my post on  3/21/06 
(https://stat.ethz.ch/pipermail/bioconductor/2006-March/012421.html). I get 
an error when trying to load Biobase itself, or when loading one of the 
packages that depend on it (see below for examples and sessionInfo) using 
an .Rprofile file in the working directory that is automatically sourced 
upon starting R. The error appears to happen because of a problem with the 
Windows menu in the Rgui, i.e., not finding functions "winMenuNames" or 
""winMenuAddItem". I know Windows is not the ideal OS for R, but I'm stuck 
with it for a while... I should also point out that the error message does 
not always appear if you are loading several different libraries, in 
particular when "library(RWinEdt)" comes first, which can lead to problems 
with functions later like the one I put in my original post. RWinEdt also 
adds an item on to the menu but doesn't seem to have any problems, so 
perhaps it's doing something correctly that Biobase is not doing?

Thanks,
Jenny

Example 1) This is with just "library(affy) in the .Rprofile file, although 
"library(Biobase)" alone produces the same error message:

R : Copyright 2006, The R Foundation for Statistical Computing
Version 2.3.0 (2006-04-24)
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Loading required package: affy
Loading required package: Biobase
Loading required package: tools
Loading required package: methods

Welcome to Bioconductor


     Vignettes contain introductory material.

     To view, simply type 'openVignette()' or start with 'help(Biobase)'.

     For details on reading vignettes, see the openVignette help page.


Error in inherits(x, "factor") : could not find function "winMenuNames"
Error: .onAttach failed in 'attachNamespace'
Error: package 'Biobase' could not be loaded

 > source(".rprofile")
Loading required package: affy
Loading required package: Biobase

Welcome to Bioconductor


     Vignettes contain introductory material.

     To view, simply type 'openVignette()' or start with 'help(Biobase)'.

     For details on reading vignettes, see the openVignette help page.


Loading required package: affyio
Loading required package: matchprobes
 > sessionInfo()
Version 2.3.0 (2006-04-24)
i386-pc-mingw32

attached base packages:
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
[7] "tools"     "base"

other attached packages:
       gcrma matchprobes        affy      affyio     Biobase
     "2.4.0"     "1.4.0"    "1.10.0"     "1.0.0"    "1.10.0"
 >


Example 2) With only "library(limma)" in the .Rprofile (R welcome stuff 
deleted):

Loading required package: methods
Error in f(libname, pkgname) : could not find function "winMenuAddItem"
Error in library(limma) : .First.lib failed for 'limma'
 > ?winMenuAddItem
 >

Example 3) With "library(RWinEdt)" then "library(limma)" in the .Rprofile; 
no error message, but Biobase is not loaded:

Loading required package: methods
Loading required package: utils

 > sessionInfo()
Version 2.3.0 (2006-04-24)
i386-pc-mingw32

attached base packages:
[1] "stats"     "graphics"  "grDevices" "datasets"  "utils"     "methods"
[7] "base"

other attached packages:
   limma RWinEdt
"2.7.2" "1.7-4"



 >

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu