[BioC] Updating

[Iain Morrison]

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  You have an outdated biocLite() function.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?


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