[BioC] installing bioconductor

[Robert Gentleman]

Seems pretty odd - like you have a defective version of something. What 
happens if you try to install some other package via the menu (I'm 
guessing you are on windows - you might want to consult the posting 
guide for the sorts of information that is helpful e.g. the output of 
sessionInfo).
And should that work, what happens if you download affy and try to 
install from a local zip file?

Best wishes,
   Robert

Altiner, Ahmet (NIH/NCI) [G] wrote:
> 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
> 
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> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org