[BioC] GO.db for DO

[Martin Morgan]

On 03/05/2011 08:50 AM, Matthew Pocock wrote:
> OH, I see that there is a DO.db in bioconductor already:
> 
> http://www.bioconductor.org/help/bioc-views/release/data/annotation/html/DO.db.html
> 
> <http://www.bioconductor.org/help/bioc-views/release/data/annotation/html/DO.db.html>That
> is great. However, it doesn't seem to install for me.
> 
>> biocLite("DO.db")
> Using R version 2.11.1, biocinstall version 2.6.9.
> Installing Bioconductor version 2.6 packages:
> [1] "DO.db"
> Please wait...
> 
> Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
>   argument 'lib' is missing: using
> '/home/nmrp3/R/x86_64-pc-linux-gnu-library/2.11'
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>   package ‘DO.db’ is not available
> 
> It looks like I have bioconductor 2.6 but DO.db is packaged for 2.7.
> 
>> source("http://bioconductor.org/biocLite.R")
> BioC_mirror = http://www.bioconductor.org
> Change using chooseBioCmirror().
>> biocLite()
> Using R version 2.11.1, biocinstall version 2.6.9.
> Installing Bioconductor version 2.6 packages:
> [snip]
> 
> So it looks like I'm being handed bioconductor 2.6 rather than 2.7 - perhaps
> this is because I allowed Ubuntu to install R version 2.11.1?

yes, Bioconductor is versioned to correspond with R. R.2.11.* -> Bioc
2.6; R.2.12.* -> Bioc 2.7. So update your R (and installed packages,
e.g., http://bioconductor.org/install/#update-bioconductor-packages) and
you'll have access to DO.db.

Martin

> 
> Matthew
> 
> On 5 March 2011 16:14, Matthew Pocock <turingatemyhamster at gmail.com> wrote:
> 
>> Hi,
>>
>> I've been using GO.db and find it very useful. I'd now like to have a
>> similar API for the disease ontology (DO). Is there something I can read
>> that may explain how to expose the DO data as a package? I guess I'm asking
>> if there is a guide to how I would develop DO.db.
>>
>> Thanks,
>>
>> Matthew
>>
>> --
>> Matthew Pocock
>> mailto: turingatemyhamster at gmail.com
>> gchat: turingatemyhamster at gmail.com
>> msn: matthew_pocock at yahoo.co.uk
>> irc.freenode.net: drdozer
>> (0191) 2566550
>>
>>
> 
> 
> 
> 
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