[BioC] Failure to load Biobase

[Martin Morgan]

Hi Jenny --

I guess you have a line like

library("Biobase")

in .Rprofile.  From reading ?.Rprofile, it sounds like what happens is
that the code in .Rprofile gets sourced before the standard packages
are loaded. So when Biobase goes looking for winMenuNames (which is in
the 'utils' package) it doesn't find it.

The right thing to do is to have in your .Rprofile something like

local({
    old <- getOption("defaultPackages")
    options(defaultPackages = c(old, "Biobase"))
})

which adds Biobase to the list of 'default' packages.

Martin

Jenny Drnevich <drnevich at uiuc.edu> writes:

> 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
>
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