[BioC] minfi not available for R vs 2.15.1

[Dan Tenenbaum]

On Thu, Aug 9, 2012 at 11:36 AM, Christine Briggs
<Christine.Briggs at steward.org> wrote:
> Thanks Dan.
> That's how I used to install packages in my previous lab. However, our
> institutional firewall here prevents me from downloading and installing
> lumi, lima and other packages that way
> so I've had to go to the webpage for
> each package and download the source package.

I don't understand that....biocLite() just calls install.packages()
which just grabs the package via HTTP on port 80, so if you can use
your web browser, you ought to be able to do this.


> Then I use the installation
> command in my R console:
>>install.packages("lumi")
>

If you have downloaded the source package, you want to do this:
install.packages("lumi_X.Y.Z.tar.gz", repos=NULL)
where X Y and Z match the actual version number on the source package
you downloaded. But it's better to use biocLite().


> which generated the message with minfi:
>>"package 'minfi' is not available (for R version 2.15.1)".
>
> Why do you think the lines below worked in my R console this time?
>


>>source("http://bioconductor.org/biocLite.R")
>>biocLite("minfi")
>>library(minfi)

See above.
Dan


>
> Chris
>
>
>
> -----Original Message-----
> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
> Sent: Thu 09-Aug-12 11:32 AM
> To: chris briggs [guest]
> Cc: bioconductor at r-project.org; Christine Briggs
> Subject: Re: [BioC] minfi not available for R vs 2.15.1
>
> On Thu, Aug 9, 2012 at 7:27 AM, chris briggs [guest]
> <guest at bioconductor.org> wrote:
>>
>> I've just loaded the latest versions of R (2.15.1) and Bioconductor onto
>> my Mac (OSX 10.7.4) and now I'd like to install minfi. When will a
>> compatible version be available?
>>
>> Chris Briggs
>>
>>
>>  -- output of sessionInfo():
>>
>>> install.packages("minfi")
>
>
> Try this:
>
>   source("http://bioconductor.org/biocLite.R")
>   biocLite("minfi")
>
> Dan
>
>
>> Warning message:
>> package â?~minfiâ?T is not available (for R version 2.15.1)
>
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>