[BioC] installation problem / CRAN.packages deprecated warning message

Seth Falcon sfalcon at fhcrc.org
Sun Jan 22 02:15:58 CET 2006

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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