[BioC] installing bioconductor

[Altiner, Ahmet (NIH/NCI) [G]]

Thanks everyone.

I tried both suggestions, still getting error message. Both with BiocLite()
(same message -- "Error in .readRDS(pfile) : cannot read workspace version 0
written by R 2.1.1; need R 1.4.0 or newer") 
and if I use:
getBioC(groupname="affy") (which gives the error message ("Error in
install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy",  : 
        unused argument(s) (groupname ...)")

any takers?

Ahmet



-----Original Message-----
From: jon butchar [mailto:butchar.2 at osu.edu] 
Sent: Thursday, September 08, 2005 4:32 PM
To: bioconductor at stat.math.ethz.ch
Cc: Altiner, Ahmet (NIH/NCI) [G]
Subject: Re: [BioC] installing bioconductor

On Thu, 08 Sep 2005 15:12:39 -0400
"Altiner, Ahmet (NIH/NCI) [G]" <altinera at mail.nih.gov> wrote:

> As instructed on the FAQ manual, I typed in the following to R 2.1.1
> 
>  
> 
> >source(http://www.bioconductor.org/getBioC.R
> <http://www.bioconductor.org/getBioC.R> )
> 
> >getBioC("affy","release")
> 
>  
> 
> And got back the following message
> 
>  
> 
> Running getBioC version 0.8  with R version  2.1.1 
> 
>  
> 
> Running biocinstall version 1.2  with R version  2.1.1 
> 
> Error in .readRDS(pfile) : cannot read workspace version 0 written by R
> 2.1.1; need R 1.4.0 or newer
> 
>  
> 
>  
> 
> Isn't R 2.1.1 newer than R 1.4.0 ?
> 
>  
> 
>  
> 
> -Ahmet
> 

Hi.

I don't know if it's related, but getBioC.R now has a "groupName"
specification.  After sourcing the file, you could do
"> getBioC(groupname="affy")"

As James McDonald pointed out with Lite, you should also be able to do the
same with getBioC, just
"> getBioC()"

hth,

jon b