[Bioc-devel] BioC Release 2.0 REMINDER

[Vincent Carey 525-2265]

i can't reproduce it on macosx using 2.5.0 svn rev 41107
as long as I use type="source" biocLite works.

R 2.6 on linux worked also (but with the TEMPORARY message)

---
Vince Carey, PhD
Assoc. Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA
stvjc at channing.harvard.edu

On Tue, 10 Apr 2007, Seth Falcon wrote:

> Hi Martin,
>
> Martin Maechler <maechler at stat.math.ethz.ch> writes:
> > I wonder however, why
> >
> >   biocLite(.)  or biocinstalll(.)
>
> biocinstall is an implementation detail (perhaps we should hide it
> better) and should never be called directly.
>
> > do only partially work for me.
> > I get
> >
> >   Running biocinstall version 2.0.3 with R version 2.5.0 (currently in alpha)
> >   Your version of R requires version 2.0 of Bioconductor (currently in alpha too).
> >   Will install the following packages:
> >    [1] "affy"        "affydata"    "affyPLM"     "annaffy"     "annotate"
> >    [6] "Biobase"     "Biostrings"  "DynDoc"      "gcrma"       "genefilter"
> >   [11] "geneplotter" "hgu95av2"    "limma"       "marray"      "matchprobes"
> >   [16] "multtest"    "ROC"         "vsn"         "xtable"
> >   Please wait...
> >
> >   Warning: unable to access index for repository http://bioconductor.org/packages/2.0/bioc/src/contrib
> >   Warning: unable to access index for repository http://bioconductor.org/packages/2.0/data/annotation/src/contrib
> >   ...............
> >
> > and in the end nothing is installed.
> > Maybe you need to update the index file there,
> > or was I supposed not to use biocinstall() for alpha/beta
> > testing ?
>
> Can you verify that you can connect to the bioconductor.org website?
> biocLite worked for me on the 8th (from Switzerland, even) and seems
> to be working for me this morning in Seattle.
>
> It would also help to know what getOption("pkgType") says for you.
>
> Can others confirm difficulty using biocLite?
>
> Best,
>
> + seth
>
> --
> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
> http://bioconductor.org
>
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