[BioC] Error in .initContents() : couldn't find function"isGeneric"

[Straubhaar, Juerg]

Output from 3 suggested statements:

WARNING: ignoring environment value of R_HOME
 
R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.0  (2005-04-18), 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.
 
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 a HTML browser interface to help.
Type 'q()' to quit R.
 
> ls()
character(0)
> library(Biobase)
Loading required package: tools
Welcome to Bioconductor
         Vignettes contain introductory material.  To view,
         simply type: openVignette()
         For details on reading vignettes, see
         the openVignette help page.
> sessionInfo()
R version 2.1.0, 2005-04-18, i686-pc-linux-gnu
 
attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "base"
 
other attached packages:
 Biobase
"1.5.12"

My workaround is to run the history file after starting R.

Juerg Straubhaar
UMass Med


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of Seth Falcon
Sent: Fri 6/17/2005 11:38 AM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Error in .initContents() : couldn't find function"isGeneric"
 
On 17 Jun 2005, Juerg.Straubhaar at umassmed.edu wrote:

> I get the following error when starting R:
>
> Error in .initContents() : couldn't find function "isGeneric"
> Error: .onLoad failed in 'loadNamespace' for 'Biobase'
> Fatal error: unable to restore saved data in .RData
>
> I just installed R version 2.1.0 and BioC release 1.6. on a gentoo
> linux machine.  The .RData file was generated with the new version
> and distribution.
>
> When I cp .RData to a machine (gentoo linux) with R version 2.0.1,
> release 1.5, I have no difficulty starting R with the saved
> workspace image restored.
>
> The file .RData is about 30Mb.

Hmm.  So what happens if you do:

R --no-restore --vanilla
library(Biobase)
sessionInfo()

A workaround might be to load your session where you can (R 2.0.1) and
save off individual objects that you need to individual .rda files
using the save function.  Then load them into the new R using load.

+ seth

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