On Fri, Nov 5, 2010 at 9:54 AM, Robert M. Flight <rflight79@gmail.com>wrote:

> 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.
>
>
Just to add here, you can certainly install two versions of R
simultaneously.  This is one way to do a slow transition to a new version.

Sean


> Regards,
>
> -Robert
>
> On Fri, Nov 5, 2010 at 09:34, James W. MacDonald <jmacdon@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@louisville.edu
> >> EM rflight79@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
> > University of Michigan
> > Department of Human Genetics
> > 5912 Buhl
> > 1241 E. Catherine St.
> > Ann Arbor MI 48109-5618
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>
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