[BioC] Failure to load Biobase

Jenny Drnevich drnevich at uiuc.edu
Thu May 25 19:06:31 CEST 2006


Hi Martin,

Thanks for the suggestion. I'm getting better at understanding what's in 
the ?.Rprofile help page... The code below works whether it is in a file 
called ".Rprofile" in the working directory, or in a file called 
"Rprofile.site" in the $R_HOME/etc/ folder (which on my Windows system, is 
C:/Program Files/R/R-2.3.0/etc/ for those of you like me who didn't quite 
get what $R_HOME means!). I'm going to use the "Rprofile.site" method so I 
can continue to set up shortcuts to R with different default working 
directories to keep all my projects separate.

Cheers,
Jenny


At 03:27 PM 5/23/2006, Martin Morgan wrote:
>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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: 
> http://news.gmane.org/gmane.science.biology.informatics.conductor



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