[BioC] Failure to load Biobase
Martin Morgan
mtmorgan at fhcrc.org
Thu May 25 19:50:23 CEST 2006
Hi Jenny --
Probably in Windows you want to go to Start --> Settings --> Control
Panel --> System --> Advanced --> Environment variables
and create a new 'User' variable called HOME and with value equal to
the path to a directory that 'belongs' to you, e.g.,
c:\DOCUME~1\jdrnevich
Then use the file
c:\DOCUME~1\jdrnevich\.Rprofile
to store your profile information. The help page for .Rprofile says
that R will find this file. There are two advantages to doing things
this way. The first is that the .Rprofile will still be found even
after you update R. The second is that other users of your computer
don't get the 'benefit' of your customization.
('DOCUME~1' is the short name for 'Documents and Settings', and
provides a path that has no spaces in it. R handles path names with
spaces, but the 'HOME' directory is used by a number of non-windows
applications and not all of them are as smart as R. You can figure out
what the 'short' name is by going to Start --> Run --> cmd, using DOS
commands to navigate to the directory above the directory you are
interested in (in this case, c:\), and typing dir /x)
Hope that helps,
Martin
Jenny Drnevich <drnevich at uiuc.edu> writes:
> 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
More information about the Bioconductor
mailing list