[BioC] AnnotationDBI

Marc Carlson mcarlson at fhcrc.org
Fri Sep 18 21:11:27 CEST 2009

Hi Denise,

Unfortunately, I the answer to your question is no.  The annotation
packages have had to undergo some pretty major schema changes in devel
which means that they will necessarily be incompatible with the older
version of AnnotationDbi that you will find in release.  So you will
either have to use R-devel or wait a month for R-devel to become the
release version if you want to use the newer packages.  In general, I
would recommend against mixing packages from different releases as they
are not built or tested to work properly in this context.  Therefore, I
would also recommend against trying to install the newer AnnotationDbi
in the older version of R. 

For your specific case, I think you should wait a month to upgrade your
annotation packages if you can do so.  All the annotation packages are
being refreshed as we speak so that they can be current for the upcoming
release of Bioconductor.  So after the new release should be an ideal
time to upgrade.  If you can't wait that long, then you can use R-devel
with biocLite() to grab the latest packages.


Denise Mauldin wrote:
> Hey all,
> >From other posts on the list it appears that AnnotationDBI has been updated
> for the most recent R-devel.  However, I'm using the 2.5 metadata packages
> to get the best updated information for my databases and the hgu133a.db (and
> other affy) annotation packages require an AnnotationDBI that is higher than
> 1.7.8.  Is it possible to use these packages without upgrading to R-devel?
> I currently have R 2.9.1 installed and I don't really want to go to a devel
> version.  Will AnnotationDBI 1.7.13 work with R 2.9.2 or is there another
> way around this?
> Thanks,
> Denise
> 	[[alternative HTML version deleted]]
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