[Bioc-devel] XML package unavailable? or needed by annotate and graph?

[Martin Morgan]

Hi Keith -- I'm not sure why XML is not available through biocLite,
but as a temporary measure you can retrieve it from the 'CRAN extras'
repository using install.packages.

Martin

Keith Satterley <keith at wehi.EDU.AU> writes:

> When I do
>
> biocLite(dependencies=TRUE)
>
> I get a warning message saying "
> dependency ‘XML’ is not available
>
> If I try to install XML using:
>
> biocLite("XML")
>
> I get:
> Running biocinstall version 2.2.6 with R version 2.7.0 (under development)
> Your version of R requires version 2.2 of Bioconductor.
> Warning message:
> package ‘XML’ is not available
>
> On checking installed packages DESCRIPTION files, I find the lines:
>
> annotate:
> DESCRIPTION:        rae230aprobe, tkWidgets, XML (>= 0.92-2), hsahomology,
> graph:
> DESCRIPTION:Suggests: SparseM (>= 0.36), XML, RBGL
>
> Is XML available anywhere or do the annotate package and graph package need 
> their DESCRIPTION files modified?
>
>  > sessionInfo()
> R version 2.7.0 beta (2008-04-12 r45280)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.7.0
>
> cheers,
>
> Keith
>
> ========================
> Keith Satterley
> Bioinformatics Division
> The Walter and Eliza Hall Institute of Medical Research
> Parkville, Melbourne,
> Victoria, Australia
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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PO Box 19024 Seattle, WA 98109

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