[Bioc-devel] Bioc-devel Digest, Vol 37, Issue 6

[A.J. Rossini]

> From: Seth Falcon <sfalcon at fhcrc.org>
> To: Martin Maechler <maechler at stat.math.ethz.ch>
> Date: Tue, 10 Apr 2007 06:25:21 -0700
> Subject: Re: [Bioc-devel] BioC Release 2.0 REMINDER
> 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?

biocLite works for me.   From Switzerland even (using a build of
Rdevel from mid March).

best,
-tony

blindglobe at gmail.com
Muttenz, Switzerland.
"Commit early,commit often, and commit in a repository from which we
can easily roll-back your mistakes" (AJR, 4Jan05).