OK, great.  Thanks!

- David

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



On Thu, May 15, 2014 at 6:37 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 05/15/2014 01:42 PM, Dan Tenenbaum wrote:
>
>> Hi David,
>>
>> ----- Original Message -----
>>
>>> From: "David Eby" <eby@broadinstitute.org>
>>> To: bioconductor@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]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.
>> science.biology.informatics.conductor
>>
>>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>

	[[alternative HTML version deleted]]

