[BioC] sva package for R 2.13.1?

Ying Chen Ying.Chen at imclone.com
Thu Aug 18 19:12:23 CEST 2011

Hi Sean, thanks a lot for the suggestion. 

I went to your afternoon talk at the BioC2011 and I learned a lot.

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.

> 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.


-----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.


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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