[BioC] update annotations without updating bioconductor

[Robert M. Flight]

James,

Yes, perusing this list has made me realize that one should always be
wary of mixing and matching Bioconductor function versions and
annotation packages. And now that you have pointed it out, I realize
that I was being slightly silly, knowing full well that I can download
a package and install it using "R CMD INSTALL". DUH! I do this all the
time to refresh to the current version of my own packages.

Regards,

-Robert

On Fri, Nov 5, 2010 at 09:34, James W. MacDonald <jmacdon at med.umich.edu> wrote:
> Hi Robert,
>
> It's always possible to mix and match package versions - a significant
> portion of the noise on this list consists of people admonishing posters to
> use biocLite() rather than downloading and installing things.
>
> So you can always download and install the updated annotation packages, and
> they may well work OK (I don't think Marc made any changes that are not
> backward-compatible). However, you are on your own if you have any odd
> results. Caveat emptor.
>
> Best,
>
> Jim
>
>
>
> On 11/5/2010 9:18 AM, Robert M. Flight wrote:
>>
>> Hi All,
>>
>> I'm wondering if it is possible to update annotation packages without
>> updating the core bioconductor itself. For example, if I wanted to
>> update various "org.*.db" annotation packages, GO.db, and KEGG.db
>> without updating R and Bioconductor, how would I do that? I do plan to
>> update R and Bioconductor, but the system I am using and some of the
>> packages I am using took a lot to get working correctly, and I would
>> like to enable updated annotations while taking my time to upgrade R
>> and Bioconductor, without worrying too much about breaking something.
>>
>> Currently using R 2.11 and Bioconductor 2.6.
>>
>> Thanks in advance,
>>
>> Robert
>>
>> Robert M. Flight, Ph.D.
>> University of Louisville Bioinformatics Laboratory
>> University of Louisville
>> Louisville, KY
>>
>> PH 502-852-0467
>> EM robert.flight at louisville.edu
>> EM rflight79 at gmail.com
>>
>> Williams and Holland's Law:
>>        If enough data is collected, anything may be proven by
>> statistical methods.
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
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