[BioC] annotaion in bioconductor

[Seth Falcon]

Hi Carlo,

"Colantuoni, Carlo (NIH/NIMH)" <colantuc at mail.nih.gov> writes:
> Loading required package: XML
> Error in library(pkg, character.only = TRUE, logical = TRUE, lib.loc =
> lib.loc) :
>         'XML' is not a valid package -- installed < 2.0.0?
>
> is there a current working version of the XML package available for R 2.0.1
> (Win2000 in particular)? i have downloaded a few different versions that i
> found in different places online, but have not succeeded in
> installing any.

Have you tried:

install.packages("XML")

The XML package for Windows is a bit of a special case it seems and is
not available from all CRAN mirrors.

> Also, the .pdf's for the AnnBuilder vignettes on bioconductor website give
> me an error when trying to open them. not sure why.

Thanks for reporting this.  We are looking into this matter and hope
to have it resolved shortly.

> I was also wondering if the bioconductor guys are interested in adding
> accessiblity to additional databases through AnnBuilder/annotate. One that
> I'd really like to start to get data from is the HPRD
> (http://www.hprd.org/). In particular, the protein-protein intereation data
> would be very interesting to use. I think it would be of wide interest to
> the gene expression comunity, too.

Yes, there is interest in including additional databases in AnnBuilder
or a very similar package and we have recently discussed
protein-protein interaction data in particular.  So... stay tuned.

Best,

+ seth