[BioC] Updating

[Iain Morrison]

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 at 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    You have an outdated biocLite() function.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
>
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