[BioC] automatic package installs

Votruba, Patrick G. Votruba.Patrick at mayo.edu
Fri Nov 3 21:08:56 CET 2006


My colleague recently received the following error message and it has
caused some concern among our system administrators.  The
getProbePackage function tries to download and install a package that's
not locally available and fails because the user doesn't have write
permission to the library directory.  There are, however, a core group
of R users who do have write permission and we'd like to prevent
unintentional package installations.  Is there an easy way to disable
this function?

Also, this has sparked some debate as to whether bioconductor software
also automatically updates existing packages.  If so, can this also be

Do automatic package installs/updates occur for all packages or just a
subset (e.g. annotation packages)?

I apologize if this is a redundant question, but I didn't see this
addressed in the online documentation and was unable to search the mail



Patrick G. Votruba
Statistical Systems Unit
Mayo Clinic

> > library(gcrma);
> Loading required package: affy
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
>     Vignettes contain introductory material. To view, 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
> > affybatch=ReadAffy(filenames=c("/tmp/Test.cel"));
> > exprSet=gcrma(affybatch);
> Adjusting for optical effect.Done.
> Computing affinities[1] "Checking to see if your internet connection
> works..."
> Error in getProbePackage(probepackagename) :
>         You do not have write access to
> /usr/local/biotools/r/R-2.3.1/lib/R/library
> Please check your permissions or provide a different 'lib' parameter.

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