[BioC] Hostname bug?

[Henrik Bengtsson]

Seth,

can't you set the web server so that also the old URL maps to the new
one during the migration period?

/Henrik

On 9/5/06, Seth Falcon <sfalcon at fhcrc.org> wrote:
> Hi Mark,
>
> "Kimpel, Mark William" <mkimpel at iupui.edu> writes:
> > I can update packages from the Windows menu of R 2.3.1, but not from R
> > 2.4. I get the following error message:
> >
> > Warning: unable to access index for repository
> > http://www.bioconductor.org/bin/windows/contrib/2.4
> >
> > sessionInfo()
> >
> > R version 2.4.0 Under development (unstable) (2006-08-29 r39012)
> > i386-pc-mingw32
> >
> > locale:
> > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> > States.1252;LC_MONETARY=English_United
> > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> >
> > attached base packages:
> > [1] "methods"   "stats"     "graphics"  "grDevices" "utils"
> > "datasets"  "base"
>
> Thanks for the report.  We have not added the BioC 1.9 repository to
> the location that the Windows R GUI searches and hence the warning
> message (and failure to update).
>
> At present, I suspect that even in R 2.3.z, this doesn't work as
> desired because the operation only searches one of Bioconductor's
> repositories.  As a result, various dependencies will not be updated.
>
> We will look into addressing both of these issues for R 2.4 and the
> upcoming BioC release.
>
> For now, I would recommend the following to update your packages
> (should work for R 2.4 series):
>
> library("Biobase")
> update.packages(repos=biocReposList(), dependencies=TRUE)
>
> Bw,
>
> + seth
>
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