[BioC] annotaion in bioconductor

Colantuoni, Carlo (NIH/NIMH) colantuc at mail.nih.gov
Mon Mar 7 21:17:10 CET 2005

Hello All,

I am trying to use the annoation functions in bioconductor and am having a
few problems. When installing the package using the getBioC() function
several packages, including XML, can't be found. I think this is what causes
the problem later, when i try to load the AnnBuilder package and i get this
error (on Win2000):

> library(package=AnnBuilder)

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.

If I should be directing these inquiries elsewhere, just let me know.

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

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.

Carlo Colantuoni

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