[BioC] sva package for R 2.13.1?

[Sean Davis]

On Thu, Aug 18, 2011 at 1:12 PM, Ying Chen <Ying.Chen at imclone.com> wrote:
> Hi Sean, thanks a lot for the suggestion.
>
> I went to your afternoon talk at the BioC2011 and I learned a lot.

Great to hear!

> Anyway I figured out how to install it using the source file I downloaded from Jeffry Leek's website. My computer runs windows 7 so I already have ActiveTCL installed.

Thanks, Ying, for the detailed notes.  Others will definitely benefit from them.

>> install.packages("corpcor")
>> install.packages("qvalue")
>> install.packages("D:/my_sva_source_file_fold/sva_src.tar.gz",repos=NULL, type="source")
> * installing *source* package 'sva' ...
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> This is mgcv 1.7-6. For overview type 'help("mgcv-package")'.
> Loading Tcl/Tk interface ... done
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
>
> * DONE (sva)
>> library(sva)
> Loading required package: corpcor
> Loading required package: mgcv
> This is mgcv 1.7-6. For overview type 'help("mgcv-package")'.
> Loading required package: qvalue
> Loading Tcl/Tk interface ... done
>>
>
> I am a biologist and new to R and Bioconductor. I googled this forum and find a few other threads asking for help to install sva. So I hope this will help some other people new to the field.
>
> Ying
>
>
> -----Original Message-----
> From: seandavi at gmail.com [mailto:seandavi at gmail.com] On Behalf Of Sean Davis
> Sent: Wednesday, August 17, 2011 4:57 PM
> To: Ying Chen
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] sva package for R 2.13.1?
>
> Hi, Ying.  SVA is not a bioconductor package, so you will probably
> need to contact the author for a solution.
>
> Sean
>
> On Wed, Aug 17, 2011 at 4:49 PM, Ying Chen <Ying.Chen at imclone.com> wrote:
>> Hi guys,
>>
>> Is there anyone know where I can get the correct sva package for R2.13.1? I downloaded and installed the zipped sva package from author's website, but got error message when I tried to launch it.
>>
>>> utils:::menuInstallLocal()
>> package 'sva' successfully unpacked and MD5 sums checked
>>> library(sva)
>> Error: package 'sva' was built before R 2.10.0: please re-install it
>>>
>>
>> Thanks,
>>
>> Ying
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