Hi Martin, I tried the --vanilla and that didn't work, but on removing a .RData file under / everything is now working as expected. Many thanks iain -- Iain Morrison IT Manager MRC Epidemiology Unit Institute of Metabolic Science Box 285 Addenbrooke's Hospital Hills Road Cambridge CB2 0QQ Tel 01223 769200 -----Original Message----- From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: 04 February 2012 15:31 To: Iain Morrison Cc: bioconductor at r-project.org Subject: Re: [BioC] Updating On 02/03/2012 07:07 AM, Iain Morrison wrote: > Dear All, > we update our R installation via a cron job, but it fails with > > Error in eval(expr, envir, enclos) : > You have an outdated biocLite() function. Run 'rm(biocLite)' and try > again. > Calls: source ... local -> eval.parent -> eval -> eval -> eval -> eval > Execution halted > > If the commands are run directly in R or the cron script is run from a > terminal everything work as expected. > >> source("http://bioconductor.org/biocLite.R") > BiocInstaller version 1.2.1, ?biocLite for help >> biocLite(character(), ask=FALSE, checkBuilt=TRUE) > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > > > Does anyone know what I'm doing wrong? > Hi Iain -- likely there is a function biocLite defined in a user or system .Rprofile or .RData or similar; if in .Rprofile it should probably be removed, perhaps replaced with library(BiocInstaller). Your script should probably start R with --vanilla, so that these files are not input. Hope that helps. Martin > cron script > ----------- > > #!/bin/sh > > unset DISPLAY > > /usr/local/bin/R CMD BATCH -q /usr/local/lib/R/scripts/R_update.R > /usr/local/lib/R/scripts/R_update.Rout > > cat /usr/local/lib/R/scripts/R_update.Rout > > # The End > > > > /usr/local/lib/R/scripts/R_update.R > ------------------------------------ > > > options(repos=c(CRAN="http://cran.ma.imperial.ac.uk/")) > update.packages(ask=F, checkBuilt=T) > source("http://bioconductor.org/biocLite.R") > biocLite(character(), ask=FALSE, checkBuilt=TRUE) > > > The system is RHEL 6 x64. > > thanks > > iain > > -- > > Iain Morrison > IT Manager > MRC Epidemiology Unit > Institute of Metabolic Science > Box 285 > Addenbrooke's Hospital > Hills Road > Cambridge > CB2 0QQ > Tel 01223 769200 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at 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: M1-B861 Telephone: 206 667-2793