[BioC] hugene10st.db not available?

[Marc Carlson]

Hi Mark,

In the latest versions of Bioconductor, that package has been replaced
by TWO packages (depending on which revision you want to used):

hugene10stprobeset.db

<http://www.bioconductor.org/packages/2.4/data/annotation/html/hugene10stprobeset.db.html>

and

hugene10sttranscriptcluster.db
<http://www.bioconductor.org/packages/2.4/data/annotation/html/hugene10sttranscriptcluster.db.html>

You can simply go to the links above, decide which version you need, and
then use biocLite() as usual to get the package you want.


  Marc



Mark Robinson wrote:
> Hi all.
>
> I'm trying to install the hugene10st.db package.
>
> I was unsuccessful with the standard approach of:
>
> ------------------
>   
>> source("http://bioconductor.org/biocLite.R")
>>     biocLite("hugene10st.db")
>>     
> Using R version 2.9.1, biocinstall version 2.4.12.
> Installing Bioconductor version 2.4 packages:
> [1] "hugene10st.db"
> Please wait...
>
> Warning: unable to access index for repository
> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>   package 'hugene10st.db' is not available
>   
>>     biocLite("mogene10st.db")
>>     
> Using R version 2.9.1, biocinstall version 2.4.12.
> Installing Bioconductor version 2.4 packages:
> [1] "mogene10st.db"
> Please wait...
>
> Warning: unable to access index for repository
> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>   package 'mogene10st.db' is not available
>   
>>     biocLite("limma")
>>     
> Using R version 2.9.1, biocinstall version 2.4.12.
> Installing Bioconductor version 2.4 packages:
> [1] "limma"
> Please wait...
>
> Warning: unable to access index for repository
> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9
> trying URL
> 'http://bioconductor.org/packages/2.4/bioc/bin/macosx/universal/contrib/2.9/limma_2.18.2.tgz'
> Content type 'application/x-gzip' length 1121233 bytes (1.1 Mb)
> opened URL
> ==================================================
> downloaded 1.1 Mb
> ------------------
>
> ... although you can see that works for other BioC packages, so its not
> simply a connection issue.  Correspondingly, the hyperlinks to the various
> version of the package do not work for me:
>
> http://www.bioconductor.org/packages/2.4/data/annotation/html/hugene10st.db.html
>
> (The same appears true of the 2.5 links).
>
> Am I doing something silly here?
>
> Cheers,
> Mark
>
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>