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]]