[BioC] installation problem / CRAN.packages deprecated warningmessage

Belooussov, Anton anton.belooussov at roche.com
Sun Jan 22 15:16:57 CET 2006

  Hello Seth and Bart,

Have the same problem and it seems to have an effect (since Friday). I can not load 'Biobase'. Currently work with R 2.2.1, but have also tried it with the older version of R (2.2.0) with no improvement. The message that constantly appears as long as I try to load any Bioconductor package (in any configuration) is: 

Load necessary Paket: Biobase
Error in setMethod("contents", "environment", function(object, all.names) { : 
      no existing definition for function 'contents'
Error: .onLoad in 'loadNamespace' für 'Biobase' failed

  thank you in advance

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Seth Falcon
Sent: Sunday, January 22, 2006 2:16 AM
To: Bart Hooghe
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] installation problem / CRAN.packages deprecated warningmessage

Hi Bart,

On 20 Jan 2006, barth at dmbr.ugent.be wrote:
> on installation of the current bioconductor packages (on fedora core 
> 4, R version 2.2.0) no errors are appearing and everything seems fine, 
> but it ends with the following output:
> The downloaded packages are in /tmp/Rtmpf12484/downloaded_packages
> Warning message: 'CRAN.packages' is deprecated.  Use 
> available.packages' instead.  See help("Deprecated")

Thanks for pointing this out.  The warning message indicates that we need to update a part of the installation scripts, but it should not have an effect on behavior at this time.

> There's nothing to find in the given tmp directory, so finally nothing 
> seems to be stored or installed.

Hmm, did you try simply loading one of the Bioc packages from inside R?  For example,


On second thought, it might be most useful to inspect the locations where packages would most likely have been installed:


I say most likely, because if your environment had R_LIBS set, R would have used that, but most likely, whatever .libPaths() reports will be where packages will have been installed.


  + seth

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