[BioC] package ‘hugene11sttranscriptcluster.db’ is not available

[Martin Morgan]

On 05/18/2010 07:26 PM, David Lyon wrote:
> Thanks for your help Martin
> 
> sessioninfo as below:
> 
> 
>> sessionInfo()
> R version 2.10.1 (2009-12-14) 
> i486-pc-linux-gnu 
> 
> locale:
>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
>  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
>  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8   
>  [7] LC_PAPER=en_US.utf8       LC_NAME=C                
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C           
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> loaded via a namespace (and not attached):
> [1] tools_2.10.1

I think because it is not available for the R-2.10 series, perhaps
because the chip itself was released just immediately before the
corresponding Bioconductor release (I'm guessing about the explicit
reason, based on dates in the NetAffx annotation files). I found this
out with the relatively non-intuitive commands

  source('http://bioconductor.org/biocLite.R')
  pkgs = available.packages(contrib.url(biocinstallRepos()))
  rownames(pkgs)[grepl("hugene1[01]stt", rownames(pkgs))]

and similarly non-intuitive navigation from bioconductor.org through
'Software' on the left, 'BiocViews' at the top, 'AnnotationData', then
editing the URL to read '2.5' rather than 'release'.

The solution is to update to R-2.11.

Also I don't know what you're doing with this, but I'll mention oligo
and the pd.hugene.1.1.st.v1 package (again with R-2.11).

Martin

> 
> 
> 
> 
> 
> 
> ----- Original Message ----
> From: Martin Morgan <mtmorgan at fhcrc.org>
> To: David Lyon <david_lyon3 at yahoo.com>
> Cc: bioconductor at stat.math.ethz.ch
> Sent: Tue, May 18, 2010 10:22:22 PM
> Subject: Re: [BioC] package ‘hugene11sttranscriptcluster.db’ is not available
> 
> On 05/18/2010 06:15 PM, David Lyon wrote:
>> I can download and install 
>> * DONE (hugene10sttranscriptcluster.db)
>>
>> but have problems with hugene11sttranscriptcluster.db:
>>   package ‘hugene11sttranscriptcluster.db’ is not available
>>
>> Does anyone else have this problem or is there something silly that I am doing?
> 
> Hi David --
> 
>     source("http://bioconductor.org/biocLite.R")
>     biocLite("hugene11sttranscriptcluster.db")
> 
> Works for me.
> 
> What is your sessionInfo() ?
> 
> What does 'download and install' mean to you?
> 
> Martin
> 
>> sessionInfo()
> R version 2.11.0 Patched (2010-05-01 r51886)
> x86_64-unknown-linux-gnu
> 
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> loaded via a namespace (and not attached):
> [1] tools_2.11.0
> 
>>
>> thanks
>>
>>
>>
>>
>>
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> 
> 


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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