[BioC] Problems installing sva and bladderbatch

[David Iles]

Hi,

I have experienced similar issues with a number of R packages (not all from BioC - e.g. Rwave; see below) since upgrading to R 2.14 last week. 

A solution would be much appreciated - I'm in the middle of a wavelet analysis!

Dr David Iles
Institute for Integrative and Comparative Biology
University of Leeds
Leeds LS2 9JT

d.e.iles at leeds.ac.uk

> library(Rwave)
Error in library(Rwave) : 
  package ‘Rwave’ does not have a NAMESPACE and should be re-installed

> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
> 


On 11 Nov 2011, at 14:54, Martin Morgan wrote:

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