[BioC] Problems installing sva and bladderbatch

Martin Morgan mtmorgan at fhcrc.org
Fri Nov 11 15:54:06 CET 2011

On 11/11/2011 06:44 AM, James Wagner wrote:
> Hello, when trying to install these packages using biocLite, I get the
> messages  package "sva" is not available and likewise package
> "bladderbatch" is not available. With sva I was able to download the tar.gz
> file and install it using install.packages(), however with bladderbatch I
> got the message
> Error : Invalid DESCRIPTION file
> Package name and namespace differ.
> The DESCRIPTION file contained the line "namespace auto", which when I
> removed gave no further errors with the "install.packages()" command,
> however then when I run library(bladderbatch) I get the warning message:
> Warning message:
> In loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
> keep.source) :
>    package 'bladderbatch' contains no R code and then with
> data(bladderbatch) I get that data set 'bladderbatch' not found.
> What is the best way to hack the DESCRIPTION file to get bladderbatch
> actually working?

Hi James -- sounds like you are trying to use an incorrect version of R 
(2.13 or before? sva was introduced in the current release). Try 
updating and biocLite() again. Provide sessionInfo() if that doesn't 
sound like the right solution.


> Thank-you
> 	[[alternative HTML version deleted]]
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