[BioC] Trouble with install

[Jeff Gentry]

> I would like to install bioconductor base but the install script gives me
> an error message as can be seen from the following segment of my R
> session.

>  source("C:/Documents and Settings/Owner/My
> Documents/BIOCONDUCTOR/Biobase/scripts/getBioC.R")
> > getBioC(libName="all")

As a side note, it is probably better to just call:
source("http://www.bioconductor.org/getBioC.R")
getBioC(libName="all")
That way you always have the latest version.

> unable to resolve 'www.bioconductor.org'.
> Error in getPkgDisc(isDevel) : The url for BioC PACKAGES is incorrect

The "unable to resolve ..." line would seem to be a good bet as for the
source of your problem.  If it can't resolve the name via the internet, it
is a sign that your R->internet setup is broken in some way.

> The URL in the script is the following, which does not appear to exist at
> www.bioconductor.org
> URL <-
> http://www.bioconductor.org/packages/devel/distrib/PACKAGES

That's actually not the URL at all, I'm not sure where you got that as
"distrib" doesn't even appear in getBioC.R anywhere - there's no possible
way that URL could be formed :) ...  the URL it is trying to access (the
way you called getBioC()) -

http://www.bioconductor.org/repository/release1.1/package/PACKAGES

If you can access this via your web browser, the next thing to try would
be:

readLines("http://www.bioconductor.org/repository/release1.1/package/PACKAGES")

If that fails then it is indeed a problem of your R setup.

-J