[BioC] Problems installing sva and bladderbatch

[Martin Morgan]

On 11/11/2011 07:06 AM, David Iles wrote:
> 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!

Hi David --

You have a mix of current and outdated packages. One solution might be

   http://bioconductor.org/install/#update-bioconductor-packages

Martin

>
> 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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>>
>>
>> --
>> Computational Biology
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>>
>> Location: M1-B861
>> Telephone: 206 667-2793
>>
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>


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793