[BioC] Error when loading biocLite.R via Rscript

[Dan Tenenbaum]

Hi David,

----- Original Message -----
> From: "David Eby" <eby at broadinstitute.org>
> To: bioconductor at r-project.org
> Sent: Thursday, May 15, 2014 1:38:48 PM
> Subject: [BioC] Error when loading biocLite.R via Rscript
> 
> Hi,
> 
> Has biocLite.R changed recently?  We are (recently) getting errors
> using
> this non-interactively via Rscript using R 2.15.3.  Here's a minimal
> example on a fresh 2.15.3 installation:
> $ Rscript -e "sessionInfo();
> source('http://bioconductor.org/biocLite.R')"
> R version 2.15.3 (2013-03-01)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  base
> Error in value[[3L]](cond) : could not find function "is"
> Calls: source ... tryCatch -> tryCatchList -> tryCatchOne ->
> <Anonymous>
> Execution halted
> 
> This is on Mac OS X Mavericks 10.9.2, for what it's worth.
> 
> We're implementing an internal fix of just making a
> 'library(methods)" call
> ahead of the "source" call (based on this clue in the R archives:
> https://stat.ethz.ch/pipermail/r-help/2010-February/228966.html), but
> I
> figured a general note was in order as well since that script seems
> to be
> meant to support earlier versions of R along with the current
> release.
> 

As it says in that link, Rscript does not automatically load the methods package, you have to load it
manually.

It may be that the script changed to use something in the methods package and it didn't before.

Dan


> Best,
> David
> 
> David Eby
> Consultant
> Cancer Informatics Development
> Broad Institute of MIT and Harvard
> 7 Cambridge Center, Cambridge, MA 02142,
> USAhttp://www.broadinstitute.org/cancer
> 
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> 
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