[BioC] Error when loading biocLite.R via Rscript

Martin Morgan mtmorgan at fhcrc.org
Fri May 16 00:37:58 CEST 2014


On 05/15/2014 01:42 PM, Dan Tenenbaum wrote:
> 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.

Thanks David, the script did change (R-devel made 
tools:::.BioC_version_associated_with_R_version of function, rather than a 
variable, and biocLite tested this using methods::is()). I have now updated 
biocLite to use is.function(), which I think is quite old and is defined in the 
base namespace. Your internal fix should no longer be necessary.

Martin

>>
>
> 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
>>
>> 	[[alternative HTML version deleted]]
>>
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>
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